🦀 a simple program for fastq file manipulation
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | shcargo install fqkit
# or
git clone https://github.com/sharkLoc/fqkit.git
cd fqkit
cargo b --release
# mv target/release/fqkit to anywhere you want cargo install --git https://github.com/sharkLoc/fqkit.gitFqKit -- A simple and cross-platform program for fastq file manipulation
Version: 0.4.11
Authors: sharkLoc <[email protected]>
Source code: https://github.com/sharkLoc/fqkit.git
Fqkit supports reading and writing gzip (.gz) format.
Bzip2 (.bz2) format is supported since v0.3.8.
Xz (.xz) format is supported since v0.3.9.
Under the same compression level, xz has the highest compression ratio but consumes more time.
Compression level:
format range default crate
gzip 1-9 6 https://crates.io/crates/flate2
bzip2 1-9 6 https://crates.io/crates/bzip2
xz 1-9 6 https://crates.io/crates/xz2
Usage: fqkit [OPTIONS] <COMMAND>
Commands:
topn get first N records from fastq file [aliases: head]
tail get last N records from fastq file
concat concat fastq files from different lanes
subfq subsample sequences from big fastq file [aliases: sample]
select select pair-end reads by read id
trim trim fastq reads by position
adapter cut the adapter sequence on the reads
filter a simple filter for pair end fastq sqeuence
range print fastq records in a range
search search reads/motifs from fastq file
grep grep fastq sequence by read id or full name
stats summary for fastq format file [aliases: stat]
kmer a simple kmer counter
shuffle shuffle fastq sequences
size report the number sequences and bases
slide extract subsequences in sliding windows
sort sort fastq file by name/seq/gc/length
plot line plot for A T G C N percentage in read position
fq2fa translate fastq to fasta
fq2sam converts a fastq file to an unaligned SAM file
fqscore converts the fastq file quality scores
flatten flatten fastq sequences [aliases: flat]
barcode perform demultiplex for pair-end fastq reads [aliases: demux]
check check the validity of a fastq record
remove remove reads by read name
rename rename sequence id in fastq file
reverse get a reverse-complement of fastq file [aliases: rev]
split split interleaved fastq file
merge merge PE reads as interleaved fastq file
mask convert any low quality base to 'N' or other chars
split2 split fastq file by records number
gcplot get GC content result and plot
length get reads length count [aliases: len]
view view fastq file page by page
help Print this message or the help of the given subcommand(s)
Global Arguments:
--compress-level <INT> set gzip/bzip2/xz compression level 1 (compress faster) - 9 (compress better) for gzip/bzip2/xz output file, just work with option -o/--out [default: 6]
--output-type <u|g|b|x> output type for stdout: 'g' gzip; 'b' bzip2; 'x' xz; 'u' uncompressed txt format [default: u
--log <FILE> if file name specified, write log message to this file, or write to stderr
-v, --verbosity... control verbosity of logging, [-v: Error, -vv: Warn, -vvv: Info, -vvvv: Debug, -vvvvv: Trace, defalut: Debug]
Global FLAGS:
-q, --quiet be quiet and do not show any extra information
-h, --help prints help information
-V, --version prints version information
Use "fqkit help [command]" for more information about a command