---
name: "fastq-mcf"
section: "1"
platform: "linux"
package: "ea-utils"
version: "1.1.2+dfsg-9+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastq-mcf"
---

# fastq-mcf(1)

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

## NAME

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

## SYNOPSIS

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

## DESCRIPTION

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

## 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.