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fastq-mcf - ea-utils: detect levels of adapter presence, compute likelihoods and locations
of the adapters


fastq-mcf [options] <adapters.fa> <reads.fq> [mates1.fq ...]


Version: 1.04.676

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


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

SCORE,AMT Adjust score SCORE by amount AMT

SCORE Adjust scores > SCORE to SCOTE

Filtering options*:
NUM Minimum mean quality score

NUM,THR At least NUM quals > THR

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

NUM Minimum remaining length (same as -l)

PCT Homopolymer filter percent (95)

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,

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

*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.

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