Filtering and trimming of long read sequencing data.

Filtering on quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout.

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.

pip install nanofilt
pip install nanofilt --upgrade

or

conda install -c bioconda nanofilt

NanoFilt is written for Python 3.

NanoFilt [-h] [-q QUALITY] [-l LENGTH] [--headcrop HEADCROP] [--tailcrop TAILCROP]

optional arguments:  
  -h, --help            show this help message and exit  
  -s --summary SUMMARYFILE optional, the sequencing_summary file from albacore for extracting quality scores
  -q, --quality QUALITY Filter on a minimum average read quality score  
  -l, --length LENGTH   Filter on a minimum read length  
  --maxlength MAXLENGTH Filter on a maximum read length

  --headcrop HEADCROP   Trim n nucleotides from start of read  
  --tailcrop TAILCROP   Trim n nucleotides from end of read
  --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.

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.

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