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Nanofilt

Filtering and trimming of long read sequencing data.

Please be aware that NanoFilt will no longer receive any updates, as (most of) its functionality is included in chopper (which should be lots faster, too).

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Filtering on quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line.

Intended to be used:

  • directly after fastq extraction
  • prior to mapping
  • in a stream between extraction and mapping

See also my post about NanoFilt on my blog Gigabase or gigabyte.
Due to a discrepancy between calculated read quality and the quality as summarized by albacore this script takes since v1.1.0 optionally also a --summary argument. Using this argument with the sequencing_summary.txt file from albacore will do the filtering using the quality scores from the summary. It's also faster.

INSTALLATION AND UPGRADING:

pip install nanofilt
pip install nanofilt --upgrade

or

conda install -c bioconda nanofilt

NanoFilt is written for Python 3.

USAGE:

NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH]
                [--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC]
                [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP]
                [-s SUMMARY] [--readtype {1D,2D,1D2}]
                [input]

Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin.

General options:
  -h, --help            show the help and exit
  -v, --version         Print version and exit.
  --logfile LOGFILE     Specify the path and filename for the log file.
  input                 input, uncompressed fastq file (optional)

Options for filtering reads on.:
  -l, --length LENGTH   Filter on a minimum read length
  --maxlength MAXLENGTH Filter on a maximum read length
  -q, --quality QUALITY Filter on a minimum average read quality score
  --minGC MINGC         Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if
                        using summary file.
  --maxGC MAXGC         Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if
                        using summary file.

Options for trimming reads.:
  --headcrop HEADCROP   Trim n nucleotides from start of read
  --tailcrop TAILCROP   Trim n nucleotides from end of read

Input options.:
  -s, --summary SUMMARY Use albacore or guppy summary file for quality scores
  --readtype            Which read type to extract information about from summary. Options are 1D, 2D or 1D2

EXAMPLES

gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam -
gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz
gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz

I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue or open a pull request. I will usually respond within a day, or rarely within a few days.

CITATION

If you use this tool, please consider citing our publication.