DOKK / manpages / debian 10 / ea-utils / fastq-mcf.1.en
FASTQ-MCF(1) User Commands FASTQ-MCF(1)

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

This help
Output file (stats to stdout)
Log scale for adapter minimum-length-match (2.2)
% occurance threshold before adapter clipping (0.25)
Minimum clip length, overrides scaled auto (1)
Maximum adapter difference percentage (10)
Minimum remaining sequence length (19)
Maximum remaining sequence length (none)
Remove duplicate reads : Read_1 has an identical N bases (0)
sKew percentage-less-than causing cycle removal (2)
'N' (Bad read) percentage causing cycle removal (20)
quality threshold causing base removal (10)
window-size for quality trimming (1)
remove >95% homopolymer reads (no)
remove low complexity reads (no)
Set all default parameters to zero/do nothing
Force disable/enable Illumina PF filtering (auto)
Phred-scale (auto)
Don't remove N's from the fronts/ends of reads
Don't clip, just output what would be done
Number of reads to use for subsampling (300k)
Save all discarded reads to '.skip' files
Output lots of random debugging stuff

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

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, 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.

July 2015 fastq-mcf 1.1.2