Short guide

SeqFu is composed by a main program with multiple subcommands, and a set of utilities. Check the complete documentation for each tool, that contains the detailed documentation.

SeqFu has tools for:

  • Make life easier when working from the command line (seqfu head, seqfu tail, seqfu rc…)
  • Provide a visual feedback of datasets (like seqfu view)
  • Get statistics (seqfu count and seqfu stats)
  • Perform common operations with a reliable tool (seqfu interleave, seqfu deinterleave)
  • Perform specialistic operations with added ease of use or features

Main program

If invoked without parameters, SeqFu will print the list of subprograms:

SeqFu - FASTX Tools

  · count [cnt]         : count FASTA/FASTQ reads, pair-end aware
  · deinterleave [dei]  : deinterleave FASTQ
  · derep [der]         : feature-rich dereplication of FASTA/FASTQ files
  · interleave [ilv]    : interleave FASTQ pair ends
  · lanes [mrl]         : merge Illumina lanes
  · metadata [met]      : print a table of FASTQ reads (mapping files)
  · orf                 : extract ORFs from nucleotide sequences
  · sort [srt]          : sort sequences by size (uniques)
  · stats [st]          : statistics on sequence lengths

  · cat                 : concatenate FASTA/FASTQ files
  · grep                : select sequences with patterns
  · head                : print first sequences
  · rc                  : reverse complement strings or files
  · tab                 : tabulate reads to TSV (and viceversa)
  · tabcheck            : validate TSV/CSV field consistency
  · tail                : view last sequences
  · view                : view sequences with colored quality and oligo matches

Type 'seqfu version' or 'seqfu cite' to print the version and paper, respectively.
Add --help after each command to print its usage.

Core and Utilities

Preferred commands are exposed as seqfu subcommands (see Core Tools), including:

  • seqfu orf to extract ORFs from nucleotide reads/sequences
  • seqfu tabcheck to validate TSV/CSV field consistency

Compatibility binaries are still shipped for existing pipelines:

  • fu-orf (wrapper for seqfu orf)
  • fu-tabcheck (wrapper for seqfu tabcheck)
  • plus additional standalone utilities such as fu-cov, fu-homocomp, and others

See the full list of utilities.