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/
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.. |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 <https://broadinstitute.github.io/longbow/>
_.
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/
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 <https://broadinstitute.github.io/longbow/commands.html>
_.
::
# 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
The Longbow documentation page <https://broadinstitute.github.io/longbow/>
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 <https://github.com/broadinstitute/longbow/issues>
.
For information on contributing to Longbow development, visit our developer documentation <DEVELOP.md>
_.