FASTAQ(1)

💖 FASTAQ(1) 💖

okay bestie, listen up — this is the manual page for fastaq, a whole toolbox for messing with FASTA and FASTQ files. it's giving Swiss Army knife but for sequences. you're gonna be obsessed. 🧬✨

---

🌸 SYNOPSIS 🌸

fastaq <command> [options]

---

🎀 DESCRIPTION 🎀

so fastaq is not one thing, it's like a whole clique of little commands, and you call them by name. wanna know the bare minimum for any one of them? just run it with no drama:

fastaq command

and if you want the full tea — every option, every detail — use one of these two, they do the exact same thing:

fastaq command -h
fastaq command --help

✨ the commands, aka the whole squad ✨

• 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

---

that's the whole roster, and every single one of them has its own little help page waiting for you. go forth and manipulate some sequences, queen. 👑🦋

this was fastaq version 3.17.0, dated January 2026, and yeah the page itself is called FASTAQ(1). slay, bye 💅💖