SeqMan NGen uses three powerful assemblers: XNG, SNG and QNG.
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 capable of assembling data sets of any size, given sufficient disk resources and modest RAM requirements. The XNG assembler uses multiple cores, but the exact number varies over the course of the assembly.
The primary output is an assembly folder (Win) or package (Mac) containing a binary .bam file for each reference sequence to which reads could be mapped. The assembly folder also contains accessory files. Note that BAM files cannot be edited. XNG workflows include:
- Reference-guided and templated workflows.
- Reference-guided assembly with gap closure (Choose Assembly Workflow = Whole Genome; Choose Assembly Type = Reference-guided assembly with gap closure. This workflow uses both the XNG and SNG assemblers, but the output files are most similar to XNG outputs.
The SNG assembler generates finished assemblies in SeqMan Pro (.sqd) or BAM (.assembly) formats. The .sqd files are editable within SeqMan Pro, but the number of data reads is limited to 10 million or fewer. BAM files of any size can be created, but may not be edited. The SNG/SMNG assembler uses one core during assembly. SNG/SMNG workflows include:
- All de novo assemblies. SNG/SMNG generates finished assemblies in editable SeqMan Pro format.
- Reference-guided assemblies for small genome (less than 30MB) reconstruction projects where editing is required. In order to perform editing, an output format of SeqMan Pro must be selected.
In this type of assembly, XNG is used to make a first-pass assembly. Then, a version of ArrayStar’s QSeq algorithm is applied to the results to create the finished assembly.
For a list of the output files for a given workflow, see Access and Understand Output Files and its subtopics. In addition, View the Assembly Report describes how to access the most commonly-viewed output file.
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