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https://github.com/broadinstitute/longbow

Annotation and segmentation of MAS-seq data

https://github.com/broadinstitute/longbow

Science Score: 26.0%

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    Low similarity (13.1%) to scientific vocabulary

Keywords from Contributors

bioinformatics wdl genome
Last synced: 11 months ago · JSON representation

Repository

Annotation and segmentation of MAS-seq data

Basic Info
Statistics
  • Stars: 20
  • Watchers: 4
  • Forks: 4
  • Open Issues: 36
  • Releases: 55
Created over 5 years ago · Last pushed about 3 years ago
Metadata Files
Readme License

README.rst 

Longbow
"""""""

|GitHub release| |Generic badge| |PyPI version maslongbow|

.. |GitHub release| image:: https://img.shields.io/github/release/broadinstitute/longbow.svg
   :target: https://github.com/broadinstitute/longbow/releases/

.. |Generic badge| image:: https://img.shields.io/badge/Docker-v0.6.14-blue.svg
   :target: https://console.cloud.google.com/gcr/images/broad-dsp-lrma/US/lr-longbow

.. |PyPI version maslongbow| image:: https://img.shields.io/pypi/v/maslongbow.svg
   :target: https://pypi.python.org/pypi/maslongbow/

Longbow is a command line tool to process MAS-ISO-seq data. Longbow employs a generative modelling approach to accurately annotate and segment MAS-ISO-seq's concatenated full-length transcript isoforms from single-cell or bulk long read RNA sequencing libraries.

Documentation for all ``longbow`` commands can be found on the `Longbow documentation page `_.

Installation
------------

``pip`` is recommended for Longbow installation.

::

   pip install maslongbow

For a pre-built version including all dependencies, access our Docker image.

::

   docker pull us.gcr.io/broad-dsp-lrma/lr-longbow:0.6.14

To install from Github source for development, the following commands can be run.

::

   git clone https://github.com/broadinstitute/longbow.git
   pip install -e longbow/

Getting Started
---------------

The commands below illustrate the Longbow workflow on a small library of SIRVs (Spike-in RNA Variant Control Mixes). MAS-ISO-seq concatenated transcripts are annotated, segmented, and filtered using the `mas15` model.  A number of statistics and QC images are generated along the way.  Final filtered transcripts can then be aligned using standard splice-aware long read mappers (e.g. minimap2). More detail for each command can be found in the `full documentation `_.

::

    # Download a tiny test dataset (less than 300K)
    wget https://github.com/broadinstitute/longbow/raw/main/tests/test_data/mas15_test_input.bam
    wget https://github.com/broadinstitute/longbow/raw/main/tests/test_data/mas15_test_input.bam.pbi
    wget https://github.com/broadinstitute/longbow/raw/main/tests/test_data/resources/SIRV_Library.fasta

    # Basic processing workflow
    longbow annotate -m mas_15+sc_10x5p mas15_test_input.bam | \  # Annotate reads according to the mas_15+sc_10x5p model
      tee ann.bam | \                                             # Save annotated BAM for later
      longbow filter | \                                          # Filter out improperly-constructed arrays
      longbow segment | \                                         # Segment reads according to the model
      longbow extract -o filter_passed.bam                        # Extract adapter-free cDNA sequences

    # Align reads with long read aligner (e.g. minimap2, pbmm2)
    samtools fastq filter_passed.bam | \
      minimap2 -ayYL --MD -x splice:hq SIRV_Library.fasta - | \
      samtools sort > align.bam &&
      samtools index align.bam


Getting help
------------

The `Longbow documentation page `_ provides detailed descriptions of command line options and algorithmic details. If you encounter bugs or have questions/comments/concerns, please file an issue on our `Github page `_.

Developers' guide
-----------------

For information on contributing to Longbow development, visit our `developer documentation `_.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

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Committers

Last synced: 12 months ago

All Time
  • Total Commits: 241
  • Total Committers: 4
  • Avg Commits per committer: 60.25
  • Development Distribution Score (DDS): 0.606
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jonn Smith j****h 95
Kiran V Garimella k****g 77
BumpVersion Action b****n@g****s 60
James Webber j****r 9

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 48
  • Total pull requests: 56
  • Average time to close issues: 3 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 18
  • Total pull request authors: 3
  • Average comments per issue: 1.44
  • Average comments per pull request: 0.13
  • Merged pull requests: 49
  • 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
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Top Authors
Issue Authors
  • jonn-smith (25)
  • hmyh1202 (3)
  • ashokpatowary (2)
  • MVesuviusC (2)
  • sagnikbanerjee15 (2)
  • kvg (2)
  • claumer (1)
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  • jonn-smith (27)
  • kvg (15)
  • jamestwebber (14)
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bug (10) High Priority (9) enhancement (8) good first issue (2) tests (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 11 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 38
  • Total maintainers: 1
pypi.org: maslongbow

Annotation and segmentation of MAS-seq data

  • Versions: 38
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 11 Last month
Rankings
Dependent packages count: 10.1%
Stargazers count: 14.6%
Forks count: 19.2%
Dependent repos count: 21.6%
Average: 23.0%
Downloads: 49.5%
Maintainers (1)
kgarimella
Last synced: 11 months ago

Dependencies

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