Filtering and trimming of Oxford Nanopore Sequencing data
Filtering and trimming of long read sequencing data.
INSTALLATION AND UPGRADING:
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 --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.