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Filtering and trimming of long read sequencing data
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README.md

Nanofilt

Filtering and trimming of long read sequencing data.

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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.

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