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Welcome to SeqMan NGen
Welcome to SeqMan NGen
Lasergene Genomics provides everything you need for assembly and analysis of genomic, metagenomic, exomes/gene panels and transcriptomic sequencing data, and supports all popular file formats. Most workflows will start with sequence assembly in SeqMan NGen. SeqMan…
SeqMan NGen Tutorials
SeqMan NGen Tutorials
The tutorials listed below all launch from SeqMan Ultra and end with analysis in SeqMan Ultra. The tutorials are available in both this User Guide and the SeqMan Ultra User Guide. Within each tutorial is a link for downloading the corresponding data in archived (.zip)…
SeqMan NGen calculations
Appendix » SeqMan NGen calculations
This following topics describe how SeqMan NGen handles various situations or makes calculations: Calculation of match percentage Detection of structural variations Handling of repeats Handling of sex chromosomes How mer tags are chosen
Run SeqMan NGen through the command line
Appendix » Run SeqMan NGen through the command line
To create a script: Either: Use the SeqMan NGen wizard to create the script. Rather than pressing the Assemble button at the end, simply save the script. Create a text file from scratch using the commands and parameters for XNG or SNG. Save the script with the…
Part A: Setting up the assembly in SeqMan NGen
SeqMan NGen Tutorials » Whole genome reference-guided workflow with analysis in ArrayStar » Part A: Setting up the assembly in SeqMan NGen
In this part of the tutorial, you will simply read the steps but won’t follow them yourself. No data are provided, as the data set used is 16 GB in size. Launch SeqMan NGen and choose New Assembly. In the Workflow screen, choose Variant Analysis /…
Part A: Running the assembly in SeqMan NGen and viewing it in SeqMan Ultra
SeqMan NGen Tutorials » Long-read analysis with accuracy evaluation » Part A: Running the assembly in SeqMan NGen and viewing it in SeqMan Ultra
In Part A, you will use SeqMan NGen to run the assembly, then launch the results in SeqMan Ultra. Download T5_Long_Read.zip (232 MB) and extract it to any convenient location (i.e., your desktop). Part A of the tutorial will use the files MAP006-1_2D_pass.fastq…
Part A: Setting up the transcriptome assembly in SeqMan NGen
SeqMan NGen Tutorials » RNA-Seq de novo transcriptome workflow » Part A: Setting up the transcriptome assembly in SeqMan NGen
In part A of the tutorial, you will use SeqMan NGen to de novo assemble and annotate the RNA-Seq data. Download T5_RNA-Seq_DeNovo_Transcriptome.zip (147 MB) and extract it to any convenient location (i.e., your desktop). The tutorial data consist of the…
Part A: Setting up the CNV project in SeqMan NGen
SeqMan NGen Tutorials » Copy number variation (CNV) workflow with analysis in ArrayStar and GenVision Pro » Part A: Setting up the CNV project in SeqMan NGen
In this part of the tutorial, you will use the SeqMan NGen wizard to import data and run the assembly. You will then press a button to open the results in ArrayStar. Download T3_CNV.zip (1.4 GB) and extract the contents to any convenient location (e.g., your…
Part A: Creating draft genomes in SeqMan NGen and exporting a consensus from SeqMan Ultra
SeqMan NGen Tutorials » Templated long-read workflow (ARTIC) » Part A: Creating draft genomes in SeqMan NGen and exporting a consensus from SeqMan Ultra
In Part A of this tutorial, you will use raw data in PacBio CLR, PacBio HiFi or Nanopore format to create draft genome assemblies for seven SARS-CoV-2 samples using SeqMan NGen. You will then open one of the assemblies in SeqMan Ultra, generate a table of…
Part A: Setting up the RNA-Seq reference-guided assembly in SeqMan NGen
SeqMan NGen Tutorials » RNA-Seq reference-guided workflow with analysis in ArrayStar » Part A: Setting up the RNA-Seq reference-guided assembly in SeqMan NGen
In this part of the tutorial, you will learn how to set up the project in SeqMan NGen and (optionally) run the assembly. To perform the assembly in Part A, you must download a 4 GB zipped data folder that unpacks to 14.3 GB. We expect most to simply read this section,…
Part B: Viewing annotated transcripts in SeqMan Ultra
SeqMan NGen Tutorials » RNA-Seq de novo transcriptome workflow » Part B: Viewing annotated transcripts in SeqMan Ultra
In Part A, you assembled transcriptome data in SeqMan NGen, which automatically annotated the transcripts during assembly. In this part of the tutorial, you will view the transcripts that were assembled and annotated using SeqMan NGen . When you clicked the blue…
Troubleshoot failure to launch
Appendix » Troubleshoot failure to launch
If you attempt to launch SeqMan NGen, without an updated .NET Framework Service Pack 1 (Windows) or Mono package (Mac) installed, you may receive an error message, and SeqMan NGen may fail to open. The best way to ensure the correct software is installed is to perform…
Log in to Cloud Assemblies
Log in to Cloud Assemblies
To log in to Cloud Assemblies or to access the Cloud Data Drive: If you are not logged into your DNASTAR account and press a button associated with Cloud Assemblies or the Cloud Data Drive (e.g., the Add from Cloud button in the Reference Sequence screen), a popup…
Create a reference-guided assembly to use in the “SNP to Structure” workflow
Wizard screen descriptions » Workflow » De novo genome assembling and editing workflows » Create a reference-guided assembly to use in the “SNP to Structure” workflow
If you are working with reference-guided human assemblies, Lasergene’s “SNP to Structure” workflow lets you combine genomic sequencing and variant level data with structure files from the RCSB Protein Data Bank (PDB) to model point mutations on the protein…
Annotate reference sequences prior to import
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Annotate reference sequences prior to import
Using annotated reference sequences in SeqMan NGen may enable you to better analyze the identified putative SNPs when viewing your assembled project in SeqMan Pro or SeqMan Ultra. If desired, annotate your reference sequence in SeqBuilder Pro (the Lasergene application…
Manually specify an isoform prior to import
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Manually specify an isoform prior to import
By default, SeqMan NGen chooses the longest CDS as the isoform for SNP calling. If desired, you may override the automated choice by specifying the preferred isoform manually in the reference sequence. To do so, follow these steps prior to importing the reference…
Transfer Files from a Physical Computer to the Cloud
Use the DNASTAR Cloud Data Drive » Transfer Files from a Physical Computer to the Cloud
To transfer one or more files from your desktop or laptop computer to the DNASTAR Cloud: Within the Cloud Data Drive, open the folder (if any) that will contain the files you are transferring. *Note: Once a file has been transferred to the DNASTAR Cloud Data…
Remove PhiX control reads from Illumina data prior to import
Wizard screen descriptions » Workflow » De novo genome assembling and editing workflows » Remove PhiX control reads from Illumina data prior to import
During de novo assembly, contamination of Illumina data with PhiX control sequence may result in the generation of spurious contigs. For background information, see Mukherjee et al., 2015. Note that: Not all Illumina data are contaminated with PhiX. PhiX…
Transfer a Folder from a Physical Computer to the Cloud
Use the DNASTAR Cloud Data Drive » Transfer a Folder from a Physical Computer to the Cloud
To transfer a folder and its contents from your desktop or laptop computer to the DNASTAR Cloud: Within the Cloud Data Drive, open the folder (if any) that will contain the folder you are transferring. *Note: Once a folder has been transferred to the DNASTAR Cloud…
Transfer Files or Folders from the Cloud to a Physical Computer
Use the DNASTAR Cloud Data Drive » Transfer Files or Folders from the Cloud to a Physical Computer
To download files or folders from the Cloud to a physical computer: Select the files and/or folders from the upper table by clicking, Shift+clicking or Ctrl/Cmd+clicking. *Note: If you do not make a selection, you will receive a warning message after Step…
Part B: Using MegAlign Pro to determine the SARS-CoV-2 variant in an experimental sample
SeqMan NGen Tutorials » Templated long-read workflow (ARTIC) » Part B: Using MegAlign Pro to determine the SARS-CoV-2 variant in an experimental sample
This section of the tutorial is self-contained, and can be completed even if you did not do Part A. In this section of the tutorial, you will align the experimental consensus sequence exported at the end of Part A with references sequences from four SARS-CoV-2 strains…
Input Reference (Sequence, Genome, for Scaffolding, etc.)
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.)
If any version of the Reference Sequence screen appears, you must input some type of reference sequence or genome template package before proceeding further in the wizard. The screen has different names depending on the workflow you are following. Some names include:…
Scans tab
Wizard screen descriptions » Options tabs » Scans tab
The Scans tab is used to set scanning parameters. The tab can be accessed in either of two ways: From the Assembly Options screen, click the Advanced Options button then click on the Scans tab. From the Preassembly Options screen, click the Advanced Options…
Trimming tab (Assembly Options)
Wizard screen descriptions » Options tabs » Trimming tab » Trimming tab (Assembly Options)
The Trimming tab of the Assembly Options dialog is used to set parameters for the trimming phase of the assembly. To access the tab from the Assembly Options screen, click the Advanced Options button then click on the Trimming tab. Default parameters vary…
Input Sequences
Wizard screen descriptions » Input Sequences
Regardless of the name of this screen (Input Sequences, Input Short/Long Read Sequences, etc.), you must specify the required options and enter one or more read files in this dialog before proceeding to the next screen. Depending on your workflow and the version of…
RNA-seq/transcriptomics workflows
Wizard screen descriptions » Workflow » RNA-seq/transcriptomics workflows
The following table describes each of the workflows available in the RNA-seq/transcriptomics tab of the Workflow screen. Group Workflow Description Quantitative analysis RNA-seq RPKM gene expression quantification and differential…
Filter based on “P not Ref”
Wizard screen descriptions » Options tabs » Variants tab » Filter based on “P not Ref”
In reference-guided workflows, “P not Ref” is the probability that the base does not match the reference. The P not Ref cutoff can be set using “hard” and/or “soft” filters. The following table describes the wizard parameters and their corresponding…
Specify RNA-Seq options
Wizard screen descriptions » Input Sequence files » Specify RNA-Seq options
When following the reference-guided RNA-Seq workflow, the Input Sequences screen has an additional option: Stranded RNA-Seq reads. Some library preparation methods preserve the directionality of reads, i.e., reverse reads always point 5’ to 3’ in the direction of…
Specify read technology
Wizard screen descriptions » Input Sequence files » Specify read technology
To specify read technology in the Input Sequences screen, make a selection from the Read technology drop-down menu. Default values for parameters and other assembly options in subsequent panels will be based on this selection. Considerations when choosing a read…
Layout tab (Assembly or Analysis Options)
Wizard screen descriptions » Options tabs » Layout tab » Layout tab (Assembly or Analysis Options)
The Layout tab in the Assembly Options and Analysis Options dialogs is used to set parameters for the layout phase of the assembly. To access the tab from the Assembly Options or Analysis Options screens, click the Advanced Options button then click on the Layout tab.…
Input Viral Genomes
Wizard screen descriptions » Input Viral Genomes
If you select the Viral-host integration detection workflow from the Workflow screen, the wizard will include the Input Viral Genomes screen. Before proceeding, you must input one or more viral genome sequences. To learn how to add sequences from a variety of…
loadConstraint
Appendix » Run SeqMan NGen through the command line » SNG commands » File loading commands » loadConstraint
The loadConstraint command loads a constraint file. The file can be in the NCBI ancillary file format, or in the CAP3 constraint file format. SeqMan NGen uses constraint files to identify paired end reads, similar to using the setPairSpecifier command. Constraint files…
Layout tab
Wizard screen descriptions » Options tabs » Layout tab
This is the disambiguation page for “Layout tab.” In SeqMan NGen, there are three advanced options dialogs that contain a Layout tab. See the topics below for information about each version of this tab. If you reached the Layout tab this way……
Use RNA-Seq de novo transcriptome output as a reference
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Use RNA-Seq de novo transcriptome output as a reference
You may use the contigs output from an RNA-seq de novo workflow as reference sequences in the templated RNA-Seq workflow. Doing this may allow you to quantify the relative abundances of transcripts using ArrayStar. Note that this use case assumes the same reads are…
Alignment tab
Wizard screen descriptions » Options tabs » Alignment tab
This is the disambiguation page for “Alignment tab.” In SeqMan NGen, there are three advanced options dialogs that contain an Alignment tab. See the topics below for information about each version of this tab. If you reached the Alignment tab this…
Trimming tab (Preassembly Options, all others)
Wizard screen descriptions » Options tabs » Trimming tab » Trimming tab (Preassembly Options, all others)
The Trimming tab is used to set parameters for the trimming phase of the assembly. To access the tab from the Preassembly Options screen, click the Advanced Options button then click on the Trimming tab. Default parameters vary according to the sequencing…
Appendix
Appendix
The Appendix contains the following topics: Non-English keyboards SeqMan NGen calculations Access and understand output files Turn off usage logging Installed Lasergene file locations Research references Run SeqMan NGen through the command…
Handling of repeats
Appendix » SeqMan NGen calculations » Handling of repeats
Repeat handling parameters compute a threshold for deciding the number of identical subsequences of bases (mers) used to indicate a putative repeat. Mers that are common to two or more fragment reads are aligned to determine the overall layout of reads. For additional…
RNA-Seq reference-guided workflow with analysis in ArrayStar
SeqMan NGen Tutorials » RNA-Seq reference-guided workflow with analysis in ArrayStar
RNA-Seq uses next-gen sequencing to show the presence and quantity of RNA in a genome at a particular moment. DNASTAR’s SeqMan NGen application is the starting point for both reference-guided and de novo RNA-Seq workflows. Because this tutorial involves a…
fixedTrim
Appendix » Run SeqMan NGen through the command line » SNG commands » Preprocessing and assembling commands » fixedTrim
The fixedTrim command trims reads prior to assembly using fixed values. Based on the parameter settings for this command, SeqMan NGen will trim reads either by a specified number of bases from each end, or to a specified range. Parameter Description…
Options tabs
Wizard screen descriptions » Options tabs
Multi-tabbed advanced options dialogs are available from the: Preassembly Options screen for long-read workflows, by pressing the Advanced Assembly Options button. The following tabs are available: Alignment, Layout. Preassembly Options screen for all other…
Long-read analysis with accuracy evaluation
SeqMan NGen Tutorials » Long-read analysis with accuracy evaluation
The following tutorial shows how to do long read assembly in SeqMan NGen, and contains optional steps for assembly validation in QUAST (Quality Assessment Tool for Genome Assemblies). The sequence data consists of an Oxford Nanopore Technologies (ONT) MAP006-1 .fastq…
Navigate between wizard screens
Navigate between wizard screens
There are two different ways to navigate between screens in the SeqMan NGen wizard. If you have already visited a particular screen, you can return to it by clicking its name from the menu at the left of the SeqMan NGen wizard. The menu contains a list of wizard…
Trimming tab
Wizard screen descriptions » Options tabs » Trimming tab
This is the disambiguation page for “Trimming tab.” In SeqMan NGen, there are two advanced options dialogs that contain a Trimming tab. See the topics below for information about each version of this tab. If you reached the Trimming tab this…
Include DESeq2 or edgeR statistics
Wizard screen descriptions » Workflow » RNA-seq/transcriptomics workflows » Include DESeq2 or edgeR statistics
To view statistics from DESeq2 or edgeR in ArrayStar, you first need to create one or more SeqMan NGen assembles in which one of these statistical packages was specified as the normalization method. That specification also triggers the use of the package for…
realignContigs
Appendix » Run SeqMan NGen through the command line » SNG commands » Preprocessing and assembling commands » realignContigs
The realignContigs command causes SeqMan NGen to perform another pass through a reference-guided assembly once the initial assembly is complete, and realigns contigs as needed. (This step occurs automatically for de novo assemblies.) Using this command may improve the…
Analysis Options
Wizard screen descriptions » Analysis Options
The Analysis Options wizard screen allows you to specify the analysis parameters to use for your assembly. This screen comes in several variations, one of which is shown below: *Note: If you are setting up a gene homology alignment in MegAlign Pro, click here for…
Specifying XNG or SNG/SMNG when running a script
Appendix » Run SeqMan NGen through the command line » Specifying XNG or SNG/SMNG when running a script
SeqMan NGen utilizes several assemblers with different capabilities and scripting languages. Therefore, it is essential to match the correct assembler with the type of assembly project to be done. To specify which assembler to use to run your script, type xng or sng…
XNG, SNG, and QNG assemblers
Appendix » Run SeqMan NGen through the command line » XNG, SNG, and QNG assemblers
SeqMan NGen uses three powerful assemblers: XNG, SNG and QNG. The XNG assembler: The XNG assembler (patent pending) is used for all reference-guided assemblies. This assembler features an algorithm for fast, accurate assembly of extremely large genomes and is…
setParam
Appendix » Run SeqMan NGen through the command line » XNG commands » setParam
The setParam command adjusts the stringency of one or more of the assembling parameters for the project. SeqMan NGen will use the default values for any parameter that is not specified within the script. All of the parameters for setParam are identical to the same…
Templated long-read workflow (ARTIC Amplicon)
Wizard screen descriptions » Workflow » Variant Analysis/Resequencing workflows » Templated long-read workflow (ARTIC Amplicon)
Starting with the release of Lasergene 17.3 (2021), SeqMan NGen supports both templated and de novo assembly of long-read data from Oxford Nanopore Technologies (ONT), Pacific Biosciences (PacBio) CLR and PacBio HiFi. The templated long-read workflow, known as…
Accessing Volcano and PCA plots from an RNA-Seq assembly
Access and understand output files » Accessing Volcano and PCA plots from an RNA-Seq assembly
If you perform an RNA-Seq assembly with replicates and specify DESeq2 as the normalization method, SeqMan NGen version 17.6 and later autogenerates editable output files for volcano and principal component analysis (PCA) plots for genes and isoforms. A volcano plot…
computeSNP
Appendix » Run SeqMan NGen through the command line » XNG commands » computeSNP
Sets parameters for the SNP computation phase of the assembly. The command is designed for use with existing BAM files that have not been analyzed for SNPs, or to re-analyze an existing file with different parameters. Most of the parameters for computeSNP are…
Combine/Reanalyze Existing Assemblies
Wizard screen descriptions » Workflow » Combine/Reanalyze Existing Assemblies
The following table describes each of the workflows available in the Combine/Reanalyze Existing Assemblies tab of the Workflow screen. Group Workflow Description Combine/Reanalyze Combine existing assemblies Once you have prepared…
Contents of the -zinternal folder
Access and understand output files » Reference-guided workflow output » Contents of the .assembly package » Contents of the -reports folder » Contents of the -zinternal folder
The -zinternal folder is located in the -reports folder, which in turn is part of the XNG .assembly package. In the table below (and the nomenclature used in the sentence above), it should be understood that the project name precedes any hyphen (-) or period (.)…
Cloud Monitor
Wizard screen descriptions » Cloud Monitor
After pressing the Run assembly on the Cloud link in the Run Assembly screen, you will be taken to the Cloud Monitor screen. This is where you monitor in-progress and completed Cloud Assemblies. You can also get to this screen by launching SeqMan NGen and selecting…
Access and understand output files
Access and understand output files
The output file structure for a SeqMan NGen assembly varies depending upon the workflow. For a description of output files, see Reference-guided workflow output or De novo workflow output. Note that FASTQ files “created with the SeqMan NGen wizard will have a…
Preassembly Options for all other workflows
Wizard screen descriptions » Preassembly Options » Preassembly Options for all other workflows
*Note: Does your wizard screen look different from the image below? For the standard version of this wizard screen, see Preassembly Options for long-read workflows. If your workflow includes the standard Preassembly Options screen, you can adjust the parameters used…
Input Host Files
Wizard screen descriptions » Input Host Files
If you select the Viral-host integration detection workflow from the Workflow screen, Input Host Files will be the next screen to appear. Before proceeding, you must input the host file used to filter out reads. To learn how to add files from a variety of sources,…
Input Assembly
Wizard screen descriptions » Input Assembly
If you selected the Reference-guided scaffolding and contig joining workflow in the Workflow page, the SeqMan NGen wizard will feature a screen called Input Assembly. You must enter at least one assembly project on this page before proceeding. *Note: This screen is…
RNA-Seq de novo transcriptome workflow
SeqMan NGen Tutorials » RNA-Seq de novo transcriptome workflow
With other applications, de novo assembly of RNA-Seq data can potentially result in thousands of unlabeled contigs representing the expressed transcripts. By contrast, SeqMan NGen automatically attempts to group contigs from the same gene, and then names and…
Use editing commands in the wizard
Use editing commands in the wizard
SeqMan NGen’s basic editing commands are similar to those found in Microsoft Windows and other text editing programs. These commands may be available through context (right-click) menu options in text boxes throughout the SeqMan NGen wizard. Task…
Calculation of “match percentage”
Appendix » SeqMan NGen calculations » Calculation of “match percentage”
By default, SeqMan NGen uses a local match percentage which requires that the match percentage threshold be met in each overlapping window of 50 bases. The size of this window can be adjusted by specifying a different value for the match window parameter. To access…
How “mer tags” are chosen
Appendix » SeqMan NGen calculations » How “mer tags” are chosen
The SeqMan NGen layout algorithm relies on unique subsequences of bases, or mers, which occur in overlapping regions of fragment reads. Mers that are common to two or more fragment reads are aligned to determine the overall layout of reads. Overlapping reads have many…
Add a genome template from DNASTAR
Add and remove files in the wizard » Add a genome template from DNASTAR
If your workflow includes the Reference Sequence or Set Contaminant screen, you must add at least one reference sequence, biome genome, or genome template before proceeding. Curated and up-to-date DNASTAR genome template packages are available for common model…
Input VCF Files
Wizard screen descriptions » Input VCF Files
In certain workflows, the Input VCF Files screen prompts you to input the VCF files to be annotated. All VCF files must be the same sequence version as the reference sequence added in the Reference Sequence screen. See the following topics to learn how to: Add…
Set Up Experiments
Wizard screen descriptions » Set Up Experiments
If, in the Input Sequences screen, you choose the Experiment setup option Multi-sample, Set Up Experiments will appear as the next wizard screen. The Experiment column is pre-loaded with the “Experiment” names specified in the Input Sequences screen. If…
Whole genome reference-guided workflow with analysis in ArrayStar
SeqMan NGen Tutorials » Whole genome reference-guided workflow with analysis in ArrayStar
In this tutorial, you will look for deleterious genes in the Caucasian/Utah/Mormon father-mother-daughter trio data from the NIST Genome in a Bottle project. This is commonly referred to as the “CEPH Trio.” No data are provided for Part A of the tutorial.…
Welcome
Wizard screen descriptions » Welcome
Each time you launch SeqMan NGen, the first screen that appears is the “Welcome” screen. The top of the screen has two option buttons. Press New Assembly to set up and run an assembly project using the SeqMan NGen wizard. You will start at the…
Specify paired-end data
Wizard screen descriptions » Input Sequence files » Specify paired-end data
Depending on the workflow and the read technology selected, the Input Sequences screen may allow you to specify paired reads. To specify paired reads, check the Paired-end data box. This causes the Pair Distance dialog to pop up. Type in the pair distance and…
Use a local copy of RefSeq as a transcript annotation database
Wizard screen descriptions » Transcript Annotation Database » Use a local copy of RefSeq as a transcript annotation database
To use a local copy of RefSeq as a transcript annotation database: Download the latest version of the RefSeq package from this NCBI ftp site. Choose a de novo transcriptome RNA-seq workflow. On the Transcript Annotation Database screen, select Add or Add…
Access the DNASTAR Cloud Data Drive
Use the DNASTAR Cloud Data Drive » Access the DNASTAR Cloud Data Drive
Once you have met the license and credential requirements, the Data Drive can be accessed in several ways: Through the SeqMan NGen wizard: In the Welcome screen, select Assemble on the DNASTAR Cloud (currently available on Windows and Macintosh only) if you are…
assemble
Appendix » Run SeqMan NGen through the command line » SNG commands » Preprocessing and assembling commands » assemble
The assemble command is required and reprocesses and assembles the sequences that have been loaded. Preprocessing may include quality trimming, and scanning for vector, repetitive, and contaminant sequences. Parameter Description Allowed values…
Add a genome template from NCBI
Add and remove files in the wizard » Add a genome template from NCBI
If your workflow includes the Reference Sequence or Set Contaminant screen, you must add at least one reference sequence, biome genome, or genome template before proceeding. If you are doing a local (i.e. non-Cloud) assembly, you may download and/or add genomes…
Handling of sex chromosomes
Appendix » SeqMan NGen calculations » Handling of sex chromosomes
When using the SeqMan NGen wizard, certain workflows allow you to specify the subject’s Gender in the Assembly Options screen. *Note for command-line users: When using the command-line version of XNG, the sex of the subject is instead specified using the…
Alignment tab (Assembly Options)
Wizard screen descriptions » Options tabs » Alignment tab » Alignment tab (Assembly Options)
The Alignment tab of the Assembly Options dialog is used to set parameters for the alignment phase of the assembly. To access the tab from the Assembly Options screen, click the Advanced Options button then click on the Alignment tab. The options available in this tab…
View the Project Report
Access and understand output files » View the Project Report
The Project Report summarizes the assembly statistics, including the parameters used, the number of assembled/unassembled sequences and contigs in your project, and the average quality scores. Opening the Project Report: Use any of the methods below: Click the…
Reference-guided workflow output
Access and understand output files » Reference-guided workflow output
Reference-guided workflows vary in the number and contents of output files and folders. Only a subset of items in the table below may appear for a particular workflow. In the file names below, the project name should be understood to precede any hyphen (-) or…
Workflow
Wizard screen descriptions » Workflow
“Workflow” is the first wizard screen in SeqMan NGen and is where you select the assembly workflow. Each group of workflows is accessed by clicking its dark blue “bar-shaped” tab on the left. Click a link below for descriptions of each…
Detection of structural variations
Appendix » SeqMan NGen calculations » Detection of structural variations
In addition to SNPs and small insertions and deletions, genetic variation can also involve large scale rearrangements. These rearrangements may include large insertions and deletions, inversions, and translocations — collectively known as structural variations…
Peak Detection tab
Wizard screen descriptions » Options tabs » Peak Detection tab
The Peak Detection tab is used to set parameters for MACS peak detection. To access the tab from the Analysis Options screen, click the Advanced Analysis Options button then click on the Peak Detection tab. The options available in this tab may vary depending on the…
Variant Call Format (VCF) files workflows
Wizard screen descriptions » Workflow » Variant Call Format (VCF) files workflows
The following table describes each of the workflows available in the Variant Call Format (VCF) files tab of the Workflow screen. These workflows are used if you have assembled your data and done SNP calling in another application and have VCF files with a .vcf or .abi…
Variant Analysis/Resequencing workflows
Wizard screen descriptions » Workflow » Variant Analysis/Resequencing workflows
The following table describes each of the workflows available in the Variant Analysis/Resequencing tab of the Workflow screen. Group Workflow Description ABI / Sanger Whole genome Align Sanger trace data from one or multiple samples…
Make a custom VCF file
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Specify a VCF, BED or Manifest file » Make a custom VCF file
Variant Call Format (VCF) files have multiple uses. For instance, they can provide a way to flag previously known SNPs and to filter them in SNP tables. In DNASTAR’s SeqMan NGen, these SNPs are called "annotated SNPs"; in ArrayStar, they are referred to as "user…
Assembly Output
Wizard screen descriptions » Assembly Output
When the Assembly Output screen appears in the wizard, you must select a name and location for your project before proceeding further. *Note: If you are setting up a gene homology alignment in MegAlign Pro, click here for information on the specialized version of…
Remove a sequence from the list
Add and remove files in the wizard » Remove a sequence from the list
To remove a sequence that has been added to the list on the left of the Input Sequences screen, select the file from the list and press Remove.
RNA-Seq reference-guided workflow output
Access and understand output files » RNA-Seq reference-guided workflow output
If you are following a reference-guided RNA-Seq workflow, output results are saved in an .assembly package folder labeled with the user-specified project name and the suffix _RNA-Seq. This folder contains the following files: Subfolder Name File…
setParam
Appendix » Run SeqMan NGen through the command line » SNG commands » Parameter settings commands » setParam
The setParam command allows you to adjust the stringency of one or more of the assembling parameters for the project. SeqMan NGen will use the default values for any parameter that is not specified within the script. Parameter Description Allowed values…
Assembly Summary
Wizard screen descriptions » Assembly Summary
After a local assembly has finished in the Assembly Log, clicking Next > takes you to the Assembly Summary screen. If assembly failed, the dialog displays the message “Assembly failed. No report available.” Otherwise, you will see the Project Report…
Example regular expressions
Wizard screen descriptions » Input Sequence files » Specify paired-end data » Example regular expressions
Examples of expressions you may find useful regarding paired end naming specifications follow. Please note this is not a complete list of regular expressions, and the definitions of the terms used are limited to their application to SeqMan NGen paired end naming…
set
Appendix » Run SeqMan NGen through the command line » SNG commands » Preprocessing and assembling commands » set
The set command is used to set variables. See the example below and those under the runScript command. Example: set $snp:true set $snpMethod:”Diploid”
set
Appendix » Run SeqMan NGen through the command line » XNG commands » set
The command set is used to set variables. It does not have any associated parameters. See the example below and those under the runScript command. Example: set $snp:true set $snpMethod:”Diploid”
Installed Lasergene file locations
Appendix » Installed Lasergene file locations
The following file names use ‘x’ to represent the version number. File Category Application Path Application2 ArrayStar Windows: C:\Program Files (x86)\DNASTAR\Lasergene x\ArrayStar SeqNinja (command line) Windows:…
Alignment tab (Preassembly Options, all others)
Wizard screen descriptions » Options tabs » Alignment tab » Alignment tab (Preassembly Options, all others)
The Alignment tab is used to set parameters for the alignment phase of the assembly. To access the tab from the Preassembly Options screen, click the Advanced Options button then click on the Alignment tab. Default parameters vary according to the sequencing…
Define Binding Proteins
Wizard screen descriptions » Define Binding Proteins
This wizard screen only appears for reference-guided ChIP-seq workflows. The Define Binding Protein screen allows you to define binding sites for your experiment. Start by making a selection from the Known binding site motif drop-down menu. The Define…
Variant calling accuracy workflow
Wizard screen descriptions » Workflow » Variant Analysis/Resequencing workflows » Variant calling accuracy workflow
While SeqMan NGen 17 no longer has a workflow named “Variant calling accuracy” (AKA “validation control accuracy,” “reference SNP accuracy”), you can still perform this workflow as follows: In the Workflow screen, select the…
Layout tab (Preassembly Options, long read)
Wizard screen descriptions » Options tabs » Layout tab » Layout tab (Preassembly Options, long read)
The Layout tab of the Preassembly Options dialog is used to set parameters for the layout phase of the assembly. To access the tab from the Preassembly Options screen, click the Advanced Assembly Options button then click on the Layout tab. Default parameters vary…
Part B: Finding a putative duplication in the reference sequence using ArrayStar
SeqMan NGen Tutorials » Copy number variation (CNV) workflow with analysis in ArrayStar and GenVision Pro » Part B: Finding a putative duplication in the reference sequence using ArrayStar
In Part A of this tutorial, you ran an assembly and launched the results in ArrayStar. In this part, you will use the ArrayStar Gene Table to locate potential duplications in the reference sequence. Imagine that you would like to find a region that is repeated in the…
Non-English keyboards
Appendix » Non-English keyboards
SeqMan NGen recognizes only standard English-keyboard characters as input. If you are using a non-English keyboard, we recommend that you switch to a “virtual” English keyboard. Click a link for instructions: Windows 7 & 8, Macintosh 10.11.…
Run Assembly Project
Wizard screen descriptions » Run Assembly Project
The Run Assembly Project screen follows the Assembly Output screen and prompts you to specify a name for the project and a location in which to save temporary files. You can also review system memory information that will help you make an educated decision whether to…