wip/nanofilt 2.8.0.20210223 NetBSD

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