https://github.com/broadinstitute/umi-collapser-internal
Science Score: 26.0%
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
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (6.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: broadinstitute
- Language: Python
- Default Branch: master
- Size: 143 KB
Statistics
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
Umi-collapser
Description
Umi-collapser identifies families of molecules in scRNA-seq experiments originating from the same original molecule and merges them into a single output read, calling consensus bases for any bases covered by multiple reads
Consensus base calling
Two methods of consensus bases calling are currently supported: calculation of the posterior probabilities for each base and simple majority voting.
Inputs and Output
Umi-collapser accepts a BAM files with reads tagged by cellular and molecular barcodes and outputs a new BAM file where reads from the same family are collapsed. Reads that do not form families of more than one are output with no modification.
Example Usage
``` $ umi-collapser --help usage: umi-collapser [-h] -i INPUTBAM -o OUTPUTBAM [--inputissorted] [--cellbarcodetag CELLBARCODETAG] [--molecularbarcodetag MOLECULARBARCODETAG] [--genetag GENETAG] [--calling_method {posterior,majority}] [--verbose] [--debug]
Collapse reads from the same Gene, UMI, Cell Barcode Triplet
optional arguments: -h, --help show this help message and exit -i INPUTBAM, --inputbam INPUTBAM input bamfile -o OUTPUTBAM, --outputbam OUTPUTBAM output bamfile --inputissorted flag indicating if the input bam is sorted by tags --cellbarcodetag CELLBARCODETAG tag name for the cell barcode --molecularbarcodetag MOLECULARBARCODETAG tag name for the molecular barcode --genetag GENETAG tag name for the gene tag --calling_method {posterior,majority} method to use to call individual bases --verbose verbosity level --debug flag for debug mode
```
Ubuntu Installation
sudo apt-get install build-essential
sudo apt-get install libbz2-dev libcurl4-openssl-dev libssl-dev
python3 setup.py install
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total 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
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