FLAIR

Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.

2 shared topics • 2 shared operations

HTSeq — Python framework for high-throughput sequencing data analysis, primarily used for counting aligned reads overlapping genomic features (genes, exons) from SAM/BAM/CRAM files using GTF/GFF annot

2 shared topics • 2 shared operations

Use when working with nf-core/nanoseq — a reproducible Nextflow pipeline for Oxford Nanopore Technology (ONT) long-read sequencing data. Covers basecalling (Guppy/Dorado), alignment (minimap2), QC (Na

2 shared topics • 2 shared operations

Sailfish — rapid mapping-based isoform quantification from RNA-seq reads. Uses quasi-mapping to estimate transcript abundance without full alignment. Provides TPM and estimated counts per transcript.

2 shared topics • 2 shared operations

SortMeRNA — fast filtering of ribosomal RNA reads from metatranscriptomic and RNA-seq data using local sequence alignment against curated rRNA databases (SILVA, RFAM). CLI tool for rRNA removal, rRNA

2 shared topics • 2 shared operations