SEQKIT(1)

💖 SEQKIT(1) — bestie edition 💖

okay so. seqkit. the moment. this is the cross-platform and ultrafast toolkit for FASTA/Q file manipulation and honestly? it ate. no cap. 💅

✨ NAME ✨

seqkit — a cross-platform and ultrafast toolkit for FASTA/Q file manipulation 🦋

🌸 DESCRIPTION 🌸

SeqKit — a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. yes bestie that's the whole vibe and it's iconic.

Version: 2.1.0 ⭐

Author: Wei Shen <shenwei356@gmail.com> 👑

Documents: http://bioinf.shenwei.me/seqkit

Source code: https://github.com/shenwei356/seqkit

Please cite: https://doi.org/10.1371/journal.pone.0163962

Seqkit utlizies the pgzip (https://github.com/klauspost/pgzip) package to read and write gzip file, and the outputted gzip file would be slighty larger than files generated by GNU gzip. 🙈 so like, slightly bigger files, that's just the tradeoff, we accept it.

Seqkit writes gzip files very fast, much faster than the multi-threaded pigz, therefore there's no need to pipe the result to gzip/pigz. like it's giving speed, it's giving main character energy, just let it cook 🔥

💫 Usage: 💫

seqkit [command]

🎀 Available Commands: 🎀

• amplicon — extract amplicon (or specific region around it) via primer(s) 🧬
• bam — monitoring and online histograms of BAM record features
• common — find common sequences of multiple files by id/name/sequence
• concat — concatenate sequences with same ID from multiple files
• convert — convert FASTQ quality encoding between Sanger, Solexa and Illumina
• duplicate — duplicate sequences N times
• faidx — create FASTA index file and extract subsequence
• fish — look for short sequences in larger sequences using local alignment 🐟
• fq2fa — convert FASTQ to FASTA
• fx2tab — convert FASTA/Q to tabular format (and length, GC content, average quality...)
• genautocomplete — generate shell autocompletion script (bash|zsh|fish|powershell)
• grep — search sequences by ID/name/sequence/sequence motifs, mismatch allowed
• head — print first N FASTA/Q records
• head-genome — print sequences of the first genome with common prefixes in name
• locate — locate subsequences/motifs, mismatch allowed
• mutate — edit sequence (point mutation, insertion, deletion)
• pair — match up paired-end reads from two fastq files
• range — print FASTA/Q records in a range (start:end)
• rename — rename duplicated IDs
• replace — replace name/sequence by regular expression
• restart — reset start position for circular genome
• rmdup — remove duplicated sequences by ID/name/sequence
• sample — sample sequences by number or proportion
• sana — sanitize broken single line FASTQ files
• scat — real time recursive concatenation and streaming of fastx files
• seq — transform sequences (extract ID, filter by length, remove gaps...)
• shuffle — shuffle sequences
• sliding — extract subsequences in sliding windows
• sort — sort sequences by id/name/sequence/length
• split — split sequences into files by id/seq region/size/parts (mainly for FASTA)
• split2 — split sequences into files by size/parts (FASTA, PE/SE FASTQ)
• stats — simple statistics of FASTA/Q files
• subseq — get subsequences by region/gtf/bed, including flanking sequences
• tab2fx — convert tabular format to FASTA/Q format
• translate — translate DNA/RNA to protein sequence (supporting ambiguous bases)
• version — print version information and check for update
• watch — monitoring and online histograms of sequence features

🌈 Flags: 🌈

• --alphabet-guess-seq-length int — length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq) (default 10000)
• -h, --help — help for seqkit
• --id-ncbi — FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud...
• --id-regexp string — regular expression for parsing ID (default "^(\\S+)\\s?")
• --infile-list string — file of input files list (one file per line), if given, they are appended to files from cli arguments
• -w, --line-width int — line width when outputting FASTA format (0 for no wrap) (default 60)
• -o, --out-file string — out file ("-" for stdout, suffix .gz for gzipped out) (default "-")
• --quiet — be quiet and do not show extra information 🤫
• -t, --seq-type string — sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence) (default "auto")
• -j, --threads int — number of CPUs. can also set with environment variable SEQKIT_THREADS) (default 4)

Use "seqkit [command] --help" for more information about a command.

lowkey the move is: run a command, then run it again with --help. that's the whole strategy bestie, iykyk 🫶

👑 AUTHOR 👑

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. 💜

and that's a wrap!! seqkit 2.1.0+ds, January 2022, SEQKIT(1) — go forth and manipulate those FASTA/Q files, you absolute icon 🎀✨💖