TeselaGen

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

2 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

2 shared topics

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

2 shared topics

GATK VQSR (Variant Quality Score Recalibration) — machine learning-based variant filtering for GATK Best Practices germline pipelines. Trains a Gaussian mixture model on truth/training resource datase

2 shared topics

MetaPhlAn 4 + StrainPhlAn 4 — marker-gene-based metagenomic profiling and strain-level phylogenetics. MetaPhlAn profiles microbial communities at species level from shotgun metagenomes using ~5.1M uni

2 shared topics