The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Enhancements & fixes:
- PR #14 - Template update for nf-core/tools v3.0.2
- PR #15 - Fix logic for skip_assembly parameter
- PR #16 - Increase resources for Trinity
- PR #19 - Fix Salmon quantification when running in skip_assembly mode
- PR #24 - Update Trinity module and fix dependency issue
| Dependency | Old version | New version |
|---|---|---|
Trinity |
2.15.1 | 2.15.2 |
Initial release of nf-core/denovotranscript, created with the nf-core template.
This pipeline was created using code from avani-bhojwani/TransFuse and timslittle/nf-core-transcriptcorral. It also incorporates modules and subworkflows developed by the nf-core community.
The main features of this pipeline are:
- Pre-processing of paired-end RNA-seq reads with FastQC, fastp, and SortMeRNA
- De novo transcriptome assembly with Trinity and rnaSPAdes
- Redundancy reduction with EvidentialGene
- Quality assessment of the assembly with BUSCO, rnaQUAST, and TransRate
- Transcript-level quantification with Salmon
- Reporting of the results with MultiQC