DeepConsensus

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

2 shared topics • 2 shared operations

Herro — haplotype-aware error correction for Oxford Nanopore long reads using deep learning. Corrects ONT simplex reads to Q30+ accuracy while preserving haplotype information for diploid assembly. Us

2 shared topics • 2 shared operations

Use when working with Sei — the FunctionLab sequence-to-activity deep learning framework for predicting chromatin profiles and regulatory activity from DNA sequences. Sei takes 4096 bp DNA windows and

2 shared topics • 2 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 • 3 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

1 shared topic • 3 shared operations