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-f
|
pattern file
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-p
|
search pattern
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-v
|
invert (non-matching)
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-r
|
patterns use regular expression
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-n
|
by name
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-s
|
by seq
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-i
|
ignore case
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-n
|
print names
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-i
|
print id (instead of full header)
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-g
|
print gc content
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-G
|
print gc-skew
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-l
|
print length
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-B
|
print base content (e.g. -B AT -B N)
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-l
|
by length
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-n
|
by full name (not id)
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-s
|
by sequence
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-r
|
reverse
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-a
|
all
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-T
|
tabular (machine readable
|
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-j
|
number of threads
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-i
|
by id
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-p
|
into # parts
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-s
|
by size
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-O
|
output directory (def. is $infile.split)
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-m
|
min. length of reads to output e.g. 500 for reads over 500bp
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-M
|
max. length of reads to output e.g. 500 for reads under 500bp
|
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-n
|
only print read names
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-w
|
defines line width, 0 for no wrap (i.e. to turn into one-line fastx)
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-i
|
print ID instead of full head (shorten ID)
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faidx
|
Create fasta index file
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fq2a
|
fastq to fasta
|
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rmdup
|
remove duplicated sequences
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