fastq-mcf(1) 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
-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)
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)
-P N
Phred-scale (auto)
Don't remove N's from the fronts/ends of reads
Don't clip, just output what would be done
-C N
Number of reads to use for subsampling (300k)
Save all discarded reads to '.skip' files
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, 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.