SeqMan NGen- Next-Gen Sequence Assembly Software, De Novo Sequence Assembly Software, Reference-Guided Alignment Software
 

SeqMan NGen Supported File Types

 

Table 1: File Types Imported by SeqMan NGen for De Novo Assemblies and Templated Assemblies (Special Workflows)


File Type
File Extension (s)
Reads
Template Sequences
Layout File
Vectors, Repeats, and Contaminant Sequences
Illumina (scarf and fastq) *_qseq.txt, *.txt yes no no yes
Roche 4542 *.fas, *.fna yes yes no yes
Roche 454 Std. Flow Files2 *.sff yes yes no no
SOLiD *.gff, *.csfasta yes no yes no
Pacific Biosciences (HDF5) *bas.h5 yes yes no no
Ion Torrent *.bam, *.fastq yes yes no no
SeqMan *.sqd yes yes no no
Phred *.phd yes yes no no
Lasergene *.seq, *.sbd yes yes no yes
ABI1 *.abi, *.ab1, *.abd yes yes no yes
FASTA2 *.fas, *.nt, *.txt, *.fna yes yes no yes
FASTQ *.fasq yes yes no yes
File of Filenames *.fof yes yes yes yes
SCF2 and SCF3 *.scf yes yes no yes
Text *.txt yes yes no yes
GenBank *.gbk, *.gb yes yes no yes
GCG *.seq, *.gcg yes yes no yes

 

Table 2: File Types Imported by SeqMan NGen for Templated Assemblies (Normal Workflows)

File Type
File Extension (s)
Reads
Template Sequence
Layout File
Illumina (scarf and fastq) *_qseq.txt, *.txt yes no no
Ion Torrent *.bam, *.fastq yes no no
Pacific Biosciences (HDF5) *bas.h5 yes no no
Roche 4542 *.fas, *.fna yes no no
Roche 454 Std. Flow Files2 *.sff yes no no
SeqMan *.sqd no yes no
FASTA2 *.fas, *.nt, *.txt, *.fna yes yes no
FASTQ *.fasq yes no no
GenBank *.gbk, *.gb no yes no
BAM *.bam no no yes

1 SeqMan NGen does not support ABI files without base calls.

2 Should have an associated .qual file with the same file name and a .qual extension. The .qual file must be in the same folder with the sequence file in order for the quality scores to be used.


SeqMan NGen supports the export of data in .sqd, .bam, and .fas formats and can generate reports in .txt format.