@@ -45,7 +45,16 @@ Version: 0.3.8
4545Authors: sharkLoc < mmtinfo@163.com>
4646Source code: https://github.com/sharkLoc/fqkit.git
4747
48- Usage: fqkit.exe [OPTIONS] < COMMAND>
48+ Fqkit supports reading and writing gzip (.gz) format.
49+ Bzip2 format is supported since v0.3.8
50+
51+ Compression level:
52+ format range default crate
53+ gzip 1-9 6 https://crates.io/crates/flate2
54+ bzip 1-9 6 https://crates.io/crates/bzip2
55+
56+
57+ Usage: fqkit [OPTIONS] < COMMAND>
4958
5059Commands:
5160 topn get first N records from fastq file
@@ -65,7 +74,7 @@ Commands:
6574 fq2fa translate fastq to fasta
6675 fq2sam converts a fastq file to an unaligned SAM file
6776 fqscore converts the fastq file quality scores
68- flatten flatten fastq sequences
77+ flatten flatten fastq sequences [aliases: flat]
6978 join join paired end reads that are overlapping into a single longer read
7079 barcode split barcode for PE reads
7180 check check the validity of a fastq record
@@ -85,9 +94,9 @@ Options:
8594 -V, --version Print version
8695
8796Global Arguments:
88- --compress-level < int> set gzip compression level 1 (compress faster) - 9 (compress better) for gzip output file, just work with option -o/--out [default: 6]
97+ --compress-level < int> set gzip/bzip2 compression level 1 (compress faster) - 9 (compress better) for gzip/bzip2 output file, just work with option -o/--out [default: 6]
8998 --log < str> if file name specified, write log message to this file, or write to stderr
90- -v, --verbosity < str> control verbosity of logging, possible values: {error,warn,info,debug,trace} [default: debug]
99+ -v, --verbosity < str> control verbosity of logging, possible values: {error, warn, info, debug, trace} [default: debug]
91100
92101Global FLAGS:
93102 -q, --quiet be quiet and do not show any extra information
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