Now that we have package managers, such as Conda, the days of slogging though installations should be a thing of the past! To help make this a reality, I try my best to regularly submit tools to Bioconda. When possible I also try to contribute in the form of pull requests or commenting on issues with a solution. Below are a list of some contributions I have made.
Conda Submissions
I have created 35 (woohoo!🎉) Conda recipes for the community, and I have reviewed more than 1,000 Bioconda pull requests. If you have a tool you would like to submit to Bioconda, but are not sure where to start, please reach out! Between the Bioconda Gitter and myself (Twitter), I'm sure we can find some one to help you!
| Tool | Description | Pull Request |
|---|---|---|
| Aspera Connect | high-performance transfer client | anaconda/rpetit3 |
| assembly-scan | Generate basic stats for an assembly | bioconda/bioconda-recipes#11425 |
| bactopia | A flexible pipeline for complete analysis of bacterial genomes | bioconda/bioconda-recipes#17434 |
| Bio-Easel | Perl modules and scripts for easel sequence analysis library | bioconda/bioconda-recipes#29824 |
| clinker | gene cluster comparison figure generator | bioconda/bioconda-recipes#26043 |
| Dragonflye | Assemble bacterial isolate genomes from Nanopore reads | bioconda/bioconda-recipes#29696 |
| ena-dl | Download FASTQ files from ENA | bioconda/bioconda-recipes#17354 |
| executor | programmer friendly Python subprocess wrapper | conda-forge/staged-recipes#9457 |
| fastq-dl | Download FASTQ files from SRA or ENA repositories. | bioconda/bioconda-recipes#18252 |
| fastq-scan | Output FASTQ summary statistics in JSON format | bioconda/bioconda-recipes#11415 |
| GenoTyphi | assign genotypes to *Salmonella* Typhi genomes | bioconda/bioconda-recipes#25674 |
| illumina-cleanup | A simple pipeline for pre-processing Illumina FASTQ files | bioconda/bioconda-recipes#11481 |
| ISMapper | insertion sequence mapping software | bioconda/bioconda-recipes#14180 |
| lmas | Workflow for benchmarking traditional and metagenomic assemblers | bioconda/bioconda-recipes#33909 |
| mashpit | Sketch-based surveillance platform | bioconda/bioconda-recipes#35199 |
| NextPolish | Fast and accurately polish the genome generated by long reads | bioconda/bioconda-recipes#36582 |
| ParallelTask | A simple and lightweight parallel task engine | conda-forge/staged-recipes#19616 |
| peregrine-2021 | Long read assembler written in Rust | bioconda/bioconda-recipes/#32810 |
| pHierCC | Hierarchical clustering of cgMLST | bioconda/bioconda-recipes#37070 |
| Phirbo | predict prokaryotic hosts for phage (meta) genomic sequences | bioconda/bioconda-recipes#26144 |
| pLannotate | Tool for annotating engineered plasmids | bioconda/bioconda-recipes/#32760 |
| pmga | Command-line version of PMGA (PubMLST Genome Annotator) | bioconda/bioconda-recipes/#32801 |
| property-manager | useful property variants for Python programming | conda-forge/staged-recipes#9442 |
| RFPlasmid | predicting plasmid contigs from assemblies | bioconda/bioconda-recipes#25849 |
| Sequip | Perl module for biological sequence analysis and supporting utilities | bioconda/bioconda-recipes#29820 |
| SerotypeFinder | Identifies the serotype in total or partial sequenced isolates of E. coli | bioconda/bioconda-recipes#29718 |
| shovill-se | A fork of Shovill that includes support for single end reads | bioconda/bioconda-recipes#26040 |
| spaTyper | computational method for finding *spa* types | bioconda/bioconda-recipes#26044 |
| sra-human-scrubber | Identify and remove human reads from FASTQ files | bioconda/bioconda-recipes#29926 |
| staphopia-sccmec | A standalone version of Staphopia's SCCmec typing method | bioconda/bioconda-recipes#28214 |
| tbl2asn-forever | use tbl2asn forever by pretending that it's still 2019 | bioconda/bioconda-recipes#20073 |
| theiacov-gc | Workflow for genomic characterization of viral pathogens | bioconda/bioconda-recipes#33228 |
| titan-gc | Workflow for genomic characterization of viral pathogens | bioconda/bioconda-recipes#30099 |
| VADR | classification and annotation of viral sequences based on RefSeq | bioconda/bioconda-recipes#29855 |
| vcf-annotator | Add biological annotations to variants in a given VCF file | bioconda/bioconda-recipes#13417 |
Pull Requests
I have submitted 350 pull requests (85% merged, yay!🎉) to various open source projects. Below are my most recent pull requests. To see the full list, which also includes personal projects, please view them on Github.
| Pull Request | Description |
|---|---|
| samuell/awesome-bioinformatics-gotchas#1 | add a simple FASTQ gotcha |
| conda-forge/executor-feedstock#8 | patch recipe to support python 3.13 |
| bioconda/bioconda-recipes#51612 | add recipe for steamboat |
| bioconda/bioconda-recipes#51033 | add recipe for sizemeup |
| bioconda/bioconda-recipes#50068 | rebuild pasty |
| bioconda/bioconda-recipes#49373 | add recipe for scrubby |
| bioconda/bioconda-recipes#49372 | clermontyping use share folder |
| bioconda/bioconda-recipes#48007 | disable phone home snpeff |
| bioconda/bioconda-recipes#47664 | update recipe for genotyphi |
| bioconda/bioconda-recipes#47600 | Add recipe for sccmec |
Open pull request Merged pull request