transcriptm
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: sternp
- License: bsd-3-clause
- Language: Python
- Default Branch: master
- Size: 352 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 4
Metadata Files
README.md
TranscriptM
A metatranscriptome bioinformatics pipeline including metagenome contamination correction.
Installation (conda)
``` git clone git@github.com:sternp/transcriptm.git
cd transcriptm
conda env create -n transcriptm -f transcriptm.yaml
conda activate transcriptm
pip install -e . ```
Usage (QC, mapping, gDNA decontamination, and read counting pipeline)
``` transcriptm count -1 readsR1.fastq.gz \ -2 readsR2.fastq.gz \ -n 24 \ --ref combinedreference.fna \ --gff combinedreference.gff \ -m 128 \ -db /dir/to/bowtie21 /dir/to/bowtie22 \ -o output_directory
Specifying -g will concatenate a directory of .fna genomes into a single ref sequence and annotate with prokka (time intensive)
Alternatively, you can use pre-contructed files via --ref
Please note, currently the required format for the contig's FASTA headers are
positional arguments: {count}
optional arguments:
-h, --help show this help message and exit
--version Show version information.
--verbosity VERBOSITY
1 = critical, 2 = error, 3 = warning, 4 = info, 5 = debug. Default = 4 (logging) (default: 4)
--log LOG Output logging information to file
-1
Notes
You may need to download databases to filter contaminating reads from rRNA genes, the human genome...etc. Otherwise you can make your own Bowtie2-formatted database. You can specify multiple Bowtie2 databases in the transcriptm command, i.e. -db /dir/to/db1 /dir/to/db2
Pre-made databases can be downloaded like so: ``` conda activate transcriptm
kneaddatadatabase --download humangenome bowtie2 /work/microbiome/db/humangrch37bowtie2
Available pre-made databases:
KneadData Databases ( database : build = location )
humangenome : bowtie2 = http://huttenhower.sph.harvard.edu/kneadDatadatabases/Homosapienshg37andhumancontaminationBowtie2v0.1.tar.gz
humangenome : bmtagger = http://huttenhower.sph.harvard.edu/kneadDatadatabases/HomosapiensBMTaggerv0.1.tar.gz
humantranscriptome : bowtie2 = http://huttenhower.sph.harvard.edu/kneadDatadatabases/Homosapienshg38transcriptomeBowtie2v0.1.tar.gz
ribosomalRNA : bowtie2 = http://huttenhower.sph.harvard.edu/kneadDatadatabases/SILVA128LSUParcSSUParcribosomalRNAv0.2.tar.gz
mouseC57BL : bowtie2 = http://huttenhower.sph.harvard.edu/kneadDatadatabases/mouseC57BL6NJBowtie2_v0.1.tar.gz
```
Owner
- Login: sternp
- Kind: user
- Repositories: 1
- Profile: https://github.com/sternp
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Sternes
given-names: Peter R.
orcid: https://orcid.org/0000-0002-4456-150X
- family-names: Tyson
given-names: Gene W.
orcid: https://orcid.org/0000-0001-8559-9427
title: "TranscriptM: A metatranscriptome bioinformatics pipeline including metagenome contamination correction"
version: 0.3.1
doi: 110.5281/zenodo.11090118
date-released: 2024-04-30
GitHub Events
Total
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Last Year
- Release event: 1
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- Create event: 1
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Last synced: over 1 year ago
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Past Year
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