Input formats

• FASTA and FASTQ are detected automatically, and gzip-compressed files are read natively. There is no need to specify the format or to decompress first.
• Multi-line FASTA is supported everywhere. Multi-line FASTQ is legal but rare; commands that need strict validation (such as seqfu check --deep) say so in their help.

Standard input and output

• Commands that accept files also read the standard input: use - as the file name, or omit the file entirely where the help says so. This makes it easy to chain commands:

  seqfu cat -m 100 reads.fq.gz | seqfu head -n 1000 - | seqfu stats -
  

• Output goes to the standard output unless an output option is given, so redirect it (> out.fq) or pipe it into gzip.
• Messages, warnings and progress go to the standard error, so they never end up in your data.

Paired-end files

Commands with paired-end support (count, interleave, check, metadata, trim…) detect the second file of a pair from the name of the first. By default they look for the common Illumina tags _R1/_R2 and fall back to _1/_2. The tags can be changed with options such as --for-tag and --rev-tag.

Sample1_S1_L001_R1_001.fastq.gz   <- forward
Sample1_S1_L001_R2_001.fastq.gz   <- reverse, found automatically

Exit status

Commands return a non-zero exit status on errors (unreadable files, malformed records, invalid options, validation failures in check or tabcheck), so they can be used safely in scripts and workflow managers.

Help and version

seqfu                 # list all subcommands
seqfu stats --help    # help for one subcommand
seqfu version         # print the version
seqfu cite            # print the citation