---
name: "fastaq"
section: "1"
platform: "linux"
package: "fastaq"
version: "3.17.0-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastaq"
---

# fastaq(1)

FASTA and FASTQ file manipulation tools

## NAME

fastaq - FASTA and FASTQ file manipulation tools

## SYNOPSIS

**fastaq** *\<command\>* \[*options*\]

## DESCRIPTION0nf

To get minimal usage for a command use: fastaq command

To get full help for a command use one of: fastaq command **-h** fastaq command **--help**

Available commands:

acgtn\_only             Replace every non acgtnACGTN with an N add\_indels             Deletes or inserts bases at given position(s) caf\_to\_fastq           Converts a CAF file to FASTQ format capillary\_to\_pairs     Converts file of capillary reads to paired and unpaired files chunker                Splits sequences into equal sized chunks count\_sequences        Counts the sequences in input file deinterleave           Splits interleaved paired file into two separate files enumerate\_names        Renames sequences in a file, calling them 1,2,3... etc expand\_nucleotides     Makes every combination of degenerate nucleotides fasta\_to\_fastq         Convert FASTA and .qual to FASTQ filter                 Filter sequences to get a subset of them get\_ids                Get the ID of each sequence get\_seq\_flanking\_gaps  Gets the sequences flanking gaps interleave             Interleaves two files, output is alternating between fwd/rev reads make\_random\_contigs    Make contigs of random sequence merge                  Converts multi sequence file to a single sequence replace\_bases          Replaces all occurrences of one letter with another reverse\_complement     Reverse complement all sequences scaffolds\_to\_contigs   Creates a file of contigs from a file of scaffolds search\_for\_seq         Find all exact matches to a string (and its reverse complement) sequence\_trim          Trim exact matches to a given string off the start of every sequence sort\_by\_name           Sorts sequences in lexographical (name) order sort\_by\_size           Sorts sequences in length order split\_by\_base\_count    Split multi sequence file into separate files strip\_illumina\_suffix  Strips */1* or */2* off the end of every read name to\_boulderio           Converts to Boulder-IO format, used by primer3 to\_fake\_qual           Make fake quality scores file to\_fasta               Converts a variety of input formats to nicely formatted FASTA format to\_mira\_xml            Create an xml file from a file of reads, for use with Mira assembler to\_orfs\_gff            Writes a GFF file of open reading frames to\_perfect\_reads       Make perfect paired reads from reference to\_random\_subset       Make a random sample of sequences (and optionally mates as well) to\_tiling\_bam          Make a BAM file of reads uniformly spread across the input reference to\_unique\_by\_id        Remove duplicate sequences, based on their names. Keep longest seqs translate              Translate all sequences in input nucleotide sequences trim\_Ns\_at\_end         Trims all Ns at the start/end of all sequences trim\_contigs           Trims a set number of bases off the end of every contig trim\_ends              Trim fixed number of bases of start and/or end of every sequence version                Print version number and exit