Getz Lab Tools (ABSOLUTE, MuTect2)

FMLRC2 — FM-index Long Read Corrector version 2, a Rust-based hybrid error correction tool for long reads (PacBio CLR, Oxford Nanopore) using Illumina short reads as a correction guide. Builds a compr

2 shared topics • 2 shared operations

GATK4 — Genome Analysis Toolkit for germline and somatic short variant discovery (SNPs and indels). Industry-standard caller providing HaplotypeCaller for germline, Mutect2 for somatic, plus Base Qual

2 shared topics • 2 shared operations

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 • 2 shared operations

medaka -- neural network-based tool from Oxford Nanopore Technologies for creating consensus sequences and calling variants from nanopore sequencing data. Polishes draft assemblies from Flye, miniasm,

2 shared topics • 2 shared operations

SvABA -- structural variant and indel caller using genome-wide local assembly. Detects deletions, insertions, duplications, inversions, and complex rearrangements from short-read (Illumina) whole-geno

2 shared topics • 2 shared operations