Cenote Taker

Canopy — Bayesian phylogenetic reconstruction of tumor subclonal architecture from somatic SNVs and copy number alterations (CNAs). Uses MCMC sampling to infer cancer evolutionary trees, estimate subc

3 shared topics • 1 shared operation

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

3 shared topics • 1 shared operation

Battenberg is an R package for allele-specific subclonal copy number analysis from whole-genome sequencing (WGS) tumor/normal paired BAM files. It segments the genome into clonal and subclonal copy nu

3 shared topics

ipyrad is a Python toolkit for de novo and reference-guided assembly and genotyping of RADseq, GBS, ddRAD, 2bRAD, and other restriction enzyme-based reduced representation genomic datasets. Implements

3 shared topics

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

2 shared topics • 1 shared operation