SYNOPSIS

DESCRIPTION

Detects levels of adapter presence, computes likelihoods and locations (start, end) of the adapters. Removes the adapter sequences from the fastq file(s).

Stats go to stderr, unless -o is specified.

Specify -0 to turn off all default settings

If you specify multiple 'paired-end' inputs, then a -o option is required for each. IE: -o read1.clip.q -o read2.clip.fq

OPTIONS

-h

This help

-o FIL

Output file (stats to stdout)

-s N.N

Log scale for adapter minimum-length-match (2.2)

-t N

% occurance threshold before adapter clipping (0.25)

-m N

Minimum clip length, overrides scaled auto (1)

-p N

Maximum adapter difference percentage (10)

-l N

Minimum remaining sequence length (19)

-L N

Maximum remaining sequence length (none)

-D N

Remove duplicate reads : Read_1 has an identical N bases (0)

-k N

sKew percentage-less-than causing cycle removal (2)

-x N

'N' (Bad read) percentage causing cycle removal (20)

-q N

quality threshold causing base removal (10)

-w N

window-size for quality trimming (1)

-H

remove >95% homopolymer reads (no)

-X

remove low complexity reads (no)

-0

Set all default parameters to zero/do nothing

-U|u

Force disable/enable Illumina PF filtering (auto)

-P N

Phred-scale (auto)

-R

Don't remove N's from the fronts/ends of reads

-n

Don't clip, just output what would be done

-C N

Number of reads to use for subsampling (300k)

-S

Save all discarded reads to '.skip' files

-d

Output lots of random debugging stuff

Quality adjustment options:

--cycle-adjust

CYC,AMT Adjust cycle CYC (negative = offset from end) by amount AMT

--phred-adjust

SCORE,AMT Adjust score SCORE by amount AMT

--phred-adjust-max

SCORE Adjust scores > SCORE to SCOTE

Filtering options*:

--[mate-]qual-mean

NUM Minimum mean quality score

--[mate-]qual-gt

NUM,THR At least NUM quals > THR

--[mate-]max-ns

NUM Maxmium N-calls in a read (can be a %)

--[mate-]min-len

NUM Minimum remaining length (same as -l)

--homopolymer-pct

PCT Homopolymer filter percent (95)

--lowcomplex-pct

PCT Complexity filter percent (95)

If mate- prefix is used, then applies to second non-barcode read only

Adapter files are 'fasta' formatted:

Specify n/a to turn off adapter clipping, and just use filters

Increasing the scale makes recognition-lengths longer, a scale of 100 will force full-length recognition of adapters.

Adapter sequences with _5p in their label will match 'end's, and sequences with _3p in their label will match 'start's, otherwise the 'end' is auto-determined.

Skew is when one cycle is poor, 'skewed' toward a particular base. If any nucleotide is less than the skew percentage, then the whole cycle is removed. Disable for methyl-seq, etc.

Set the skew (-k) or N-pct (-x) to 0 to turn it off (should be done for miRNA, amplicon and other low-complexity situations!)

Duplicate read filtering is appropriate for assembly tasks, and never when read length < expected coverage. -D 50 will use 4.5GB RAM on 100m DNA reads - be careful. Great for RNA assembly.

*Quality filters are evaluated after clipping/trimming

Homopolymer filtering is a subset of low-complexity, but will not be separately tracked unless both are turned on.