nxtrim(1)

<short_description>

Section 1 nxtrim bookworm source

Description

nxtrim - <short_description>

nxtrim -1 R1.fastq.gz -2 R2.fastq.gz [options]

Program: nxtrim Version: v0.4.3 Contact: joconnell@illumina.com

-1 [ --r1 ] arg

read 1 in fastq format (gzip allowed)

-2 [ --r2 ] arg

read 2 in fastq format (gzip allowed)

-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)

This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.