software for life scientists

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	.sff, .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	.sff, .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.