Nanofilt
Filtering and trimming of long read sequencing data.
Please be aware that NanoFilt will no longer receive any updates, as (most of) its functionality is included in chopper (which should be lots faster, too).
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.gzI 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.