./wip/nanofilt, Filtering and trimming of Oxford Nanopore sequencing data

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Branch: CURRENT, Version:, Package name: NanoFilt-, Maintainer: pkgsrc-users

Filter and trim of long read sequencing data.

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 uses:

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

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.

### 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

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