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assembly_stats

Calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file.

https://github.com/miketrizna/assembly_stats

Science Score: 33.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file.

Basic Info
  • Host: GitHub
  • Owner: MikeTrizna
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 3.7 MB
Statistics
  • Stars: 14
  • Watchers: 2
  • Forks: 3
  • Open Issues: 5
  • Releases: 0
Created almost 8 years ago · Last pushed almost 6 years ago
Metadata Files
Readme License

README.md

assembly_stats

Zenodo DOI

A Python library that takes a FASTA file as input and calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file. It does this by breaking each scaffold wherever there is more than one N and then calculating statistics for both the scaffolds and contigs.

This is a re-write of fastametadataparser to speed up the old implementation, and -- most importantly -- to learn how to install Python scripts onto the Smithsonian HPC.

Installation

pip install assembly_stats

Usage

``` $ assembly_stats -h

usage: assembly_stats [-h] filename

Calculate statistics about genome assemblies.

positional arguments:
  filename    Genome file in FASTA format.

optional arguments:
  -h, --help  show this help message and exit

```

After calculating the statistics for the genome assembly, they will be printed out in JSON format.

Hoow to Cite

The assembly_stats package has been added to Zenodo in order to receive a stable DOI for citation: "10.5281/zenodo.3968774".

Please go to the Zenodo page for assembly_stats to find style-specific formatting options: https://zenodo.org/record/3968774.

Next steps

  • Add ability to save NumPy sequence length arrays for further visualization, since generating these are what takes the most time.

Owner

  • Name: Mike Trizna
  • Login: MikeTrizna
  • Kind: user
  • Location: Washington, DC
  • Company: Smithsonian Institution

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 10
  • Total Committers: 1
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Mike Trizna t****m@s****u 10
Committer Domains (Top 20 + Academic)
si.edu: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 6
  • Total pull requests: 1
  • Average time to close issues: 18 days
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MikeTrizna (4)
  • telatin (1)
  • mtntsuchiya (1)
Pull Request Authors
  • telatin (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 119 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 7
  • Total maintainers: 1
pypi.org: assembly-stats

Calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file.

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 119 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 16.5%
Average: 17.7%
Forks count: 19.1%
Downloads: 21.2%
Dependent repos count: 21.7%
Maintainers (1)
mtrizna
Last synced: 10 months ago
conda-forge.org: assembly_stats
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 24.4%
Average: 47.2%
Dependent packages count: 51.6%
Stargazers count: 53.6%
Forks count: 59.2%
Last synced: 11 months ago