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nanostat

Create statistic summary of an Oxford Nanopore read dataset

https://github.com/wdecoster/nanostat

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    DOI references
    Found 1 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Create statistic summary of an Oxford Nanopore read dataset

Basic Info
  • Host: GitHub
  • Owner: wdecoster
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 65.4 KB
Statistics
  • Stars: 117
  • Watchers: 2
  • Forks: 11
  • Open Issues: 1
  • Releases: 0
Created about 9 years ago · Last pushed almost 4 years ago
Metadata Files
Readme License

README.md

NanoStat

NanoStat is largely superseded by Cramino - a much faster alternative - and NanoStat will most probably no longer receive any updates





Calculate various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format.

Twitter URL install with conda Build Status

INSTALLATION

NanoStat is written for Python3 and will not work in Python2.7 or older.

pip install nanostat
or
conda install -c bioconda nanostat

USAGE

``` NanoStat [-h] [-v] [-o OUTDIR] [-p PREFIX] [-n NAME] [-t N] [--barcoded] --readtype {1D,2D,1D2}

Calculate statistics of long read sequencing dataset.

General options: -h, --help show the help and exit -v, --version Print version and exit. -o, --outdir OUTDIR Specify directory in which output has to be created. -p, --prefix PREFIX Specify an optional prefix to be used for the output file. -n, --name NAME Specify a filename/path for the output, stdout is the default. -t, --threads N Set the allowed number of threads to be used by the script. --tsv, Print the output in a tab-separated-values format

Input options.: --barcoded Use if you want to split the summary file by barcode --readtype {1D,2D,1D2} Which read type to extract information about from summary. Options are 1D, 2D, 1D2

Input data sources, one of these is required.: --fastq file [file ...] Data is in one or more (compressed) fastq file(s). --fasta file [file ...] Data is in one or more (compressed) fasta file(s). --summary file [file ...] Data is in one or more (compressed) summary file(s)generated by albacore or guppy. --bam file [file ...] Data is in one or more sorted bam file(s).

EXAMPLES: NanoStat --fastq reads.fastq.gz --outdir statreports NanoStat --summary sequencingsummary1.txt sequencingsummary2.txtsequencing_summary3.txt --readtype 1D2 NanoStat --bam alignment.bam alignment2.bam ```

EXAMPLES

NanoStat --fastq reads.fastq.gz --outdir statreports NanoStat --summary sequencing_summary1.txt sequencing_summary2.txt sequencing_summary3.txt --readtype 1D2 NanoStat --bam alignment.bam alignment2.bam

Example output

``` General summary:
Active channels: 502 Mean read length: 8593.5 Mean read quality: 10.8 Median read length: 5168.0 Median read quality: 11.2 Number of reads: 408254 Read length N50: 15141 Total bases: 3508315665 Number, percentage and megabases of reads above quality cutoffs

Q5: 406428 (99.6%) 3502.0Mb Q7: 395016 (96.8%) 3234.5Mb Q10: 305509 (74.8%) 2475.9Mb Q12: 87903 (21.5%) 422.9Mb Q15: 124 (0.0%) 0.1Mb Top 5 highest mean basecall quality scores and their read lengths 1: 16.2 (407; a803bcfc-9d7a-4a87-84e4-1a0296113700) 2: 16.2 (880; f5fee32a-9471-4a68-8697-a71887599757) 3: 16.1 (729; 3ea23a79-641e-41ab-bb5b-c22609977136) 4: 16.1 (1057; b0cef5fd-c5e1-4539-9591-b7376b2953e8) 5: 15.8 (841; 3d4f8075-6151-4147-bdc3-e5d53ff66084) Top 5 longest reads and their mean basecall quality score 1: 255821 (6.8; 7d069f04-d4db-4f12-a1b9-c19d70993492) 2: 254573 (7.1; a245999b-de28-4720-a8c3-0d5cbb26e473) 3: 253711 (7.0; a84b106b-13d3-4bfa-b548-71a47c9032c3) 4: 245784 (7.0; 2a60ee11-8793-46c1-a3d9-667bc4e70405) 5: 245776 (7.1; 72a8cf33-75fd-4c07-8a4c-7516b690938b) ```

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

Bioinformatics postdoc using short and long read sequencing in neurodegenerative disorders at Rademakers Lab

GitHub Events

Total
  • Issues event: 3
  • Watch event: 29
  • Issue comment event: 2
Last Year
  • Issues event: 3
  • Watch event: 29
  • Issue comment event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 86
  • Total Committers: 4
  • Avg Commits per committer: 21.5
  • Development Distribution Score (DDS): 0.291
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
wdecoster d****r@g****m 61
wdecoster w****r@m****e 23
Andreas Sjödin a****n@g****m 1
flashton2003 f****n@g****m 1
Committer Domains (Top 20 + Academic)
molgen.vib-ua.be: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 37
  • Total pull requests: 7
  • Average time to close issues: 3 months
  • Average time to close pull requests: 16 minutes
  • Total issue authors: 33
  • Total pull request authors: 3
  • Average comments per issue: 4.03
  • Average comments per pull request: 0.43
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mbhall88 (2)
  • mw55309 (2)
  • devonorourke (2)
  • tolot27 (2)
  • SimonHegele (1)
  • asmmahmoud (1)
  • APZPM (1)
  • flashton2003 (1)
  • wdecoster (1)
  • kapsakcj (1)
  • WellJoea (1)
  • lmolokin (1)
  • Dymphan (1)
  • shashibioinfo143 (1)
  • MingDeakin (1)
Pull Request Authors
  • wdecoster (5)
  • druvus (1)
  • flashton2003 (1)
Top Labels
Issue Labels
enhancement (4) question (1) bug (1) wontfix (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 176 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 29
  • Total maintainers: 2
pypi.org: nanostat

Calculate statistics for Oxford Nanopore sequencing data and alignments

  • Versions: 28
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 176 Last month
Rankings
Stargazers count: 8.1%
Dependent packages count: 10.0%
Forks count: 10.5%
Average: 10.7%
Dependent repos count: 11.6%
Downloads: 13.3%
Maintainers (1)
wdecoster
Last synced: 12 months ago
spack.io: py-nanostat

Calculate statistics for Oxford Nanopore sequencing data and alignments

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Average: 28.8%
Dependent packages count: 57.7%
Maintainers (1)
Pandapip1
Last synced: 12 months ago

Dependencies

setup.py pypi
  • nanoget >=1.13.2
  • nanomath >=1.0.0