Projects | Open Source Science

Projects

Updated 6 months ago

multiqc • Rank 24.6 • Science 77%

Aggregate results from bioinformatics analyses across many samples into a single report.

analysis bioconda bioinformatics data-visualization multiqc pypi python quality-control reporting seqera vizualisation

Updated 6 months ago

hgtseq • Rank 5.1 • Science 67%

A pipeline to investigate horizontal gene transfer from NGS data

bwa-mem bwa-mem2 fastqc genomics-visualization ggbio horizontal-gene-transfer kraken2 krona multiqc nextflow nf-core ngs pipeline samtools taxonomies tidyverse workflow

Updated 6 months ago

taxtriage • Rank 5.8 • Science 49%

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.

classification metagenomics multiqc taxonomy triage

Updated 5 months ago

https://github.com/becavin-lab/checkatlas • Rank 4.3 • Science 36%

One liner tool to check the quality of your single-cell atlases.

control multiqc python quality scanpy seurat single-cell

Updated 6 months ago

dropseqpipe • Rank 9.5 • Science 10%

A SingleCell RNASeq pre-processing snakemake workflow

conda drop-seq dropseq dropseqtools multiqc picard pipeline plot reference-genome scrb-seq scrbseq snakemake star umi yaml

Updated 6 months ago

fair_bowtie2_mapping • Science 44%

Align reads over a reference genome, filter aligned-reads, and mark duplicates

bowtie2 multiqc sambamba snakemake snakemake-workflow snakemake-wrappers

Updated 6 months ago

aspen • Science 49%

CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲

atac-seq-pipeline genrich macs2 multiqc ngs-pipeline