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sam2lca

sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files - Published in JOSS (2022)

https://github.com/maxibor/sam2lca

Science Score: 93.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 11 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 6 months ago · JSON representation

Repository

Lowest Common Ancestor from a SAM/BAM/CRAM alignment file

Basic Info
  • Host: GitHub
  • Owner: maxibor
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 95.5 MB
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 4
  • Open Issues: 1
  • Releases: 13
Created over 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

DOI DOI badge

sam2lca

Lowest Common Ancestor from a SAM/BAM/CRAM sequence alignment file.

TLDR

Analysis of sequencing reads aligned to a DNA database with NCBI accession numbers, using the NCBI taxonomy

bash sam2lca analyze myfile.bam

See all options

bash sam2lca --help sam2lca update-db --help sam2lca list-db --help sam2lca analyze --help

For further infos, check out the sam2lca documentation and tutorial

Installation

With Conda (recommended)

bash conda install -c bioconda sam2lca

With pip

bash pip install sam2lca

For development purposes, from the dev branch

```bash

clone repository

git clone git@github.com:maxibor/sam2lca.git

work on the dev branch

git checkout dev

work in the sam2lca conda environment

conda env create -f environment.yml conda activate sam2lca

install sam2lca in editable mode

pip install -e .

Run the unit and integration tests

pytest -s -vv --script-launch-mode=subprocess ```

or

bash pip install git+ssh://git@github.com/maxibor/sam2lca.git@dev

Documentation

The documentation of sam2lca, including tutorials, is available here: sam2lca.readthedocs.io

Cite

sam2lca has been published in JOSS with the following DOI: 10.21105/joss.04360

bixtex @article{Borry2022, doi = {10.21105/joss.04360}, url = {https://doi.org/10.21105/joss.04360}, year = {2022}, publisher = {The Open Journal}, volume = {7}, number = {74}, pages = {4360}, author = {Maxime Borry and Alexander Hübner and Christina Warinner}, title = {sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files}, journal = {Journal of Open Source Software} }

Owner

  • Name: Maxime Borry
  • Login: maxibor
  • Kind: user
  • Location: Mainz, Germany
  • Company: TRON - Translational Oncology Mainz

Bioinformatics Scientist

JOSS Publication

sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files
Published
June 01, 2022
DOI
Volume 7, Issue 74, Page 4360
Authors
Maxime Borry ORCID
Microbiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany
Alexander Hübner ORCID
Microbiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany
Christina Warinner ORCID
Microbiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany, Department of Anthropology, Harvard University, Cambridge, MA, United States of America
Editor
Jacob Schreiber ORCID
Tags
metagenomics microbiome alignment sam bam cram htslib taxonomy LCA ancestor
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GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 188
  • Total Committers: 3
  • Avg Commits per committer: 62.667
  • Development Distribution Score (DDS): 0.053
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
maxibor m****y@g****m 178
Alex Huebner a****r@g****m 9
Francesco Asnicar f****r@g****m 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 9
  • Average time to close issues: 11 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 2.57
  • Average comments per pull request: 0.67
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • alexhbnr (2)
  • guoyuh (1)
  • jfy133 (1)
  • ZoePochon (1)
  • wyc661217 (1)
  • marouenbg (1)
Pull Request Authors
  • alexhbnr (6)
  • maxibor (1)
  • fasnicar (1)
  • kdm9 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 28 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 14
  • Total maintainers: 1
pypi.org: sam2lca

Lowest Common Ancestor on SAM/BAM/CRAM alignment files

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 28 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 15.4%
Average: 17.9%
Stargazers count: 19.4%
Dependent repos count: 21.6%
Downloads: 23.2%
Maintainers (1)
maxibor
Last synced: 6 months ago

Dependencies

setup.py pypi
  • click *
  • numpy *
  • pandas *
  • pysam *
  • python-rocksdb *
  • scipy *
  • taxopy *
  • tqdm *
  • xopen *
.github/workflows/publish_pypi.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/sam2lca_ci.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
docs/tutorial/environment.yaml pypi
environment.yml pypi