Cheatography
https://cheatography.com
A quick seqkit cheat sheet for the commands I use the most
grep-f | pattern file | -p | search pattern | -v | invert (non-matching) | -r | patterns use regular expression | -n | by name | -s | by seq | -i | ignore case |
search sequences by pattern(s) of name or sequence motifs fx2tab-n | print names | -i | print id (instead of full head | -g | print gc content | -G | print gc-skew | -l | print length | -B | print base content (e.g. -B AT -B N) |
sort-l | by length | -n | by full name (not id) | -s | by sequence | -r | reverse |
| | seq-m | min. length of reads to output e.g. 500 for reads over 500bp | -M | max. length of reads to output e.g. 500 for reads under 500bp | -n | only print read names | -w | defines line width, 0 for no wrap (i.e. to turn into one-line fastx) | -i | print ID instead of full head (shorten ID) |
stats-a | all | -T | tabular (machine readable | -j | number of threads |
split-i | by id | -p | into # parts | -s | by size | -O | output directory (def. is $infile.split) |
use split2 for fastq/paired end (-1 + -2 for paired end) otherfaidx | Create fasta index file | fq2a | fastq to fasta | rmdup | remove duplicated sequences |
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