Provided by: seqkit_2.8.2+ds-1_amd64 
NAME
seqkit - cross-platform and ultrafast toolkit for FASTA/Q file manipulation
DESCRIPTION
SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
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.
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.
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.
AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage
of the program.