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Cheatography

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

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)

other

faidx
Create fasta index file
fq2a
fastq to fasta
rmdup
remove duplicated sequences
 

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