GAPIT

BPNet — deep learning framework for learning base-resolution regulatory sequence features from genomics assays (ChIP-seq, ATAC-seq, CUT&RUN). Uses dilated convolutional neural networks to predict TF b

1 shared topic • 3 shared operations

GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-

1 shared topic • 2 shared operations

KMC — high-performance disk-based k-mer counting and set operations for genomic sequences. Counts k-mers in FASTQ, FASTA, BAM, and KMC database files with minimal memory usage via disk-based partition

1 shared topic • 2 shared operations

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

1 shared topic • 2 shared operations

Sarek — nf-core Nextflow pipeline for germline and somatic variant calling from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing data. Supports multiple variant cal

1 shared topic • 2 shared operations