Copyright © 2016, Illumina, Inc. All rights reserved. See LICENSE for further details.
Requiredarguments:-1 [ --r1 ] arg
read 1 in fastq format (gzip allowed)
-2 [ --r2 ] arg
read 2 in fastq format (gzip allowed)
Allowedoptions:-O [ --output-prefix ] arg
output prefix
--justmp
just creates a the mp/unknown libraries (reads with adapter at the start will be completely N
masked)
--stdout
print trimmed reads to stdout (equivalent to justmp)
--stdout-mp
print only known MP reads to stdout (good for scaffolding)
--stdout-un
print only unknown reads to stdout
--rf leave mate pair reads in RF orientation [by default are flipped into FR]
--preserve-mp
preserve MPs even when the corresponding PE has longer reads
--ignorePF
ignore chastity/purity filters in read headers
--separate
output paired reads in separate files (prefix_R1/prefix_r2). Default is interleaved.
-a, --aggressive
more aggressive adapter search (see docs/adapter.md)
-s, --similarity arg (=0.85)
The minimum similarity between strings to be considered a match (Hamming distance divided by
string length)
-v, --minoverlap arg (=12)
The minimum overlap to be considered for matching
-l, --minlength arg
(=21) The minimum read length to output (smaller reads will be filtered)