LSHTM Pipelines

Snippy — rapid haploid variant calling pipeline for bacterial genomics. Maps paired-end or single-end reads to a reference genome using BWA-MEM and Minimap2, calls SNPs, MNPs, and indels via Freebayes

2 shared topics • 3 shared operations

Conda and Mamba package/environment management for bioinformatics. Create, export, and reproduce isolated software environments using conda or mamba (fast C++ solver). Manage Bioconda channels, resolv

3 shared topics • 1 shared operation

nf-core/eager is a Nextflow pipeline for ancient DNA (aDNA) and palaeogenomics analysis. Handles adapter trimming, low-complexity filtering, read mapping with BWA-aln (optimal for short aDNA reads), d

3 shared topics • 1 shared operation

Poetry is the Python dependency management and packaging tool for creating reproducible projects with pyproject.toml and poetry.lock. Use this skill for dependency resolution, virtual environment isol

3 shared topics • 1 shared operation

SOAPdenovo2 — de novo short-read genome assembler for large plant and animal genomes using de Bruijn graph construction. Runs a four-stage pipeline: pregraph (k-mer graph), contig (initial contigs), m

3 shared topics • 1 shared operation