Longbow
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:0.5.37
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 mas15v2 mas15_test_input.bam | \ # Annotate reads according to the mas15v2 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.
1 maintainer
Metadata
1 maintainer
Release files for maslongbow 0.5.37
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| maslongbow-0.5.37.tar.gz | 1.1 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| maslongbow-0.5.37-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 1.2 MB
Release files / maslongbow-0.5.37.tar.gz
| Download URL | maslongbow-0.5.37.tar.gz |
|---|---|
| Size | 1.1 MB |
| Tags | Source |
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Release files / maslongbow-0.5.37-py2.py3-none-any.whl
| Download URL | maslongbow-0.5.37-py2.py3-none-any.whl |
|---|---|
| Size | 100.8 kB |
| Tags | Python 2 Python 3 |
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