Science Score: 23.0%
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✓DOI references
Found 1 DOI reference(s) in README -
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1 of 3 committers (33.3%) from academic institutions -
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Low similarity (8.4%) to scientific vocabulary
Repository
Filtering and trimming of long read sequencing data
Basic Info
Statistics
- Stars: 208
- Watchers: 9
- Forks: 15
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
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
bash
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.
Owner
- Name: Wouter De Coster
- Login: wdecoster
- Kind: user
- Location: Antwerp, Belgium
- Company: VIB-UAntwerp
- Website: https://gigabaseorgigabyte.wordpress.com/
- Twitter: wouter_decoster
- Repositories: 57
- Profile: https://github.com/wdecoster
Bioinformatics postdoc using short and long read sequencing in neurodegenerative disorders at Rademakers Lab
GitHub Events
Total
- Watch event: 23
- Fork event: 1
Last Year
- Watch event: 23
- Fork event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| wdecoster | d****r@g****m | 109 |
| Mick Watson | m****n@r****k | 3 |
| Alexander Van Uffelen | v****r@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 59
- Total pull requests: 8
- Average time to close issues: 3 months
- Average time to close pull requests: 35 minutes
- Total issue authors: 53
- Total pull request authors: 3
- Average comments per issue: 3.81
- Average comments per pull request: 0.25
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: 2 days
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 2.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- damioresegun (3)
- Adamtaranto (3)
- fizwit (2)
- tolot27 (2)
- xujiaweiouc (1)
- Kata-Pa (1)
- el-mat (1)
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- Potatoconomy (1)
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- eyesmo (1)
Pull Request Authors
- wdecoster (6)
- alvanuffelen (1)
- mw55309 (1)
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Packages
- Total packages: 1
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Total downloads:
- pypi 408 last-month
- Total dependent packages: 0
- Total dependent repositories: 2
- Total versions: 34
- Total maintainers: 1
pypi.org: nanofilt
Filtering and trimming of Oxford Nanopore Sequencing data
- Homepage: https://github.com/wdecoster/nanofilt
- Documentation: https://nanofilt.readthedocs.io/
- License: GPLv3
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Latest release: 2.8.0
published over 5 years ago
Rankings
Maintainers (1)
Dependencies
- biopython *
- pandas >=0.22.0