@GitHub @Twitter @LinkedIn @Impactstory @ORCID @Google Scholar @rss

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!

ToolDescriptionPull Request
Aspera Connecthigh-performance transfer clientanaconda/rpetit3
assembly-scanGenerate basic stats for an assemblybioconda/bioconda-recipes#11425
bactopiaA flexible pipeline for complete analysis of bacterial genomesbioconda/bioconda-recipes#17434
Bio-EaselPerl modules and scripts for easel sequence analysis librarybioconda/bioconda-recipes#29824
clinkergene cluster comparison figure generatorbioconda/bioconda-recipes#26043
DragonflyeAssemble bacterial isolate genomes from Nanopore readsbioconda/bioconda-recipes#29696
ena-dlDownload FASTQ files from ENAbioconda/bioconda-recipes#17354
executorprogrammer friendly Python subprocess wrapperconda-forge/staged-recipes#9457
fastq-dlDownload FASTQ files from SRA or ENA repositories.bioconda/bioconda-recipes#18252
fastq-scanOutput FASTQ summary statistics in JSON formatbioconda/bioconda-recipes#11415
GenoTyphiassign genotypes to *Salmonella* Typhi genomesbioconda/bioconda-recipes#25674
illumina-cleanupA simple pipeline for pre-processing Illumina FASTQ filesbioconda/bioconda-recipes#11481
ISMapperinsertion sequence mapping softwarebioconda/bioconda-recipes#14180
lmasWorkflow for benchmarking traditional and metagenomic assemblersbioconda/bioconda-recipes#33909
mashpitSketch-based surveillance platformbioconda/bioconda-recipes#35199
NextPolishFast and accurately polish the genome generated by long readsbioconda/bioconda-recipes#36582
ParallelTaskA simple and lightweight parallel task engineconda-forge/staged-recipes#19616
peregrine-2021Long read assembler written in Rustbioconda/bioconda-recipes/#32810
pHierCCHierarchical clustering of cgMLSTbioconda/bioconda-recipes#37070
Phirbopredict prokaryotic hosts for phage (meta) genomic sequencesbioconda/bioconda-recipes#26144
pLannotateTool for annotating engineered plasmidsbioconda/bioconda-recipes/#32760
pmgaCommand-line version of PMGA (PubMLST Genome Annotator)bioconda/bioconda-recipes/#32801
property-manageruseful property variants for Python programmingconda-forge/staged-recipes#9442
RFPlasmidpredicting plasmid contigs from assembliesbioconda/bioconda-recipes#25849
SequipPerl module for biological sequence analysis and supporting utilitiesbioconda/bioconda-recipes#29820
SerotypeFinderIdentifies the serotype in total or partial sequenced isolates of E. colibioconda/bioconda-recipes#29718
shovill-seA fork of Shovill that includes support for single end readsbioconda/bioconda-recipes#26040
spaTypercomputational method for finding *spa* typesbioconda/bioconda-recipes#26044
sra-human-scrubberIdentify and remove human reads from FASTQ filesbioconda/bioconda-recipes#29926
staphopia-sccmecA standalone version of Staphopia's SCCmec typing methodbioconda/bioconda-recipes#28214
tbl2asn-foreveruse tbl2asn forever by pretending that it's still 2019bioconda/bioconda-recipes#20073
theiacov-gcWorkflow for genomic characterization of viral pathogensbioconda/bioconda-recipes#33228
titan-gcWorkflow for genomic characterization of viral pathogensbioconda/bioconda-recipes#30099
VADRclassification and annotation of viral sequences based on RefSeqbioconda/bioconda-recipes#29855
vcf-annotatorAdd biological annotations to variants in a given VCF filebioconda/bioconda-recipes#13417

Pull Requests

I have submitted 269 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 RequestDescription
bioconda/bioconda-recipes#37144Set Nextpolish build to generic
lskatz/EToKi#1Allow multiple path parameters on the configure step
bioconda/bioconda-recipes#37070add recipe for pHierCC
bioconda/bioconda-recipes#37069add recipe for EToKi
nf-core/modules#2005add module for pbptyper
nf-core/modules#2003add module for pasty
nf-core/modules#2000[update] bump Bakta to 1.5.0
bioconda/bioconda-recipes#36582add recipe for NextPolish
bioconda/bioconda-recipes#36222add recipe for pbptyper
theiagen/public_health_viral_genomics#158add miniwdl check workflow

Open pull request Merged pull request