Nanofilt
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. 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.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.
CITATION
If you use this tool, please consider citing our publication.
1 maintainer
Metadata
1 maintainer
Release files for NanoFilt 2.8.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| NanoFilt-2.8.0.tar.gz | 7.4 kB | Details |
Release files / NanoFilt-2.8.0.tar.gz
| Download URL | NanoFilt-2.8.0.tar.gz |
|---|---|
| Size | 7.4 kB |
| Tags | Source |
|
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