Oxford Nanopore Technologies (ONT)

AlleleSeq — pipeline for detecting allele-specific expression (ASE) and allele-specific binding (ASB) from RNA-seq and ChIP-seq data at heterozygous SNP positions. Constructs a personal diploid genome

2 shared topics • 2 shared operations

Use when performing HLA typing from RNA-seq data with arcasHLA. Covers extracting HLA reads from STAR-aligned BAMs, high-resolution genotyping at 6-digit allele level, partial genotyping for low-cover

2 shared topics • 2 shared operations

Use when working with the ARTIC viral amplicon sequencing command-line pipeline for Oxford Nanopore data. Covers documented `artic minion`, `artic guppyplex`, and `artic_get_models` workflows for prim

2 shared topics • 2 shared operations

Loom — HDF5-based file format and Python library (loompy) for storing and accessing large single-cell RNA-seq datasets. Supports sparse/dense matrices, row attributes (genes/features), column attribut

2 shared topics • 2 shared operations

Novocraft suite — short-read alignment and BAM sorting for DNA-seq and RNA-seq. novoalign maps Illumina, Ion Torrent, and 454 reads to indexed reference genomes with Smith-Waterman scoring for high-ac

2 shared topics • 2 shared operations