NextDenovo

Canu — long-read de novo genome assembler for PacBio HiFi, PacBio CLR, and Oxford Nanopore reads. Performs read correction, trimming, and overlap-layout-consensus assembly in three stages. Supports di

2 shared topics • 1 shared operation

Getz Lab tools (ABSOLUTE, MuTect/MuTect2) from the Broad Institute for cancer genomics. ABSOLUTE infers tumor purity, ploidy, and absolute copy numbers from segmented copy number data. MuTect2 (GATK4)

2 shared topics • 1 shared operation

Jellyfish — fast, multi-threaded k-mer counter for DNA sequences. Counts exact k-mer frequencies in FASTA/FASTQ files using a lock-free hash table. Used for genome size estimation (flow cytometry-free

2 shared topics • 1 shared operation

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 • 1 shared operation

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 • 1 shared operation