TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 53.2K citations · Full text

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim, Ben Langmead, Steven L. Salzberg · Nature Methods · 2015 · 24.9K citations · Full text

Hardware Security, Engineering, Hardware Acceleration +7

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N. Dewey · BMC Bioinformatics · 2011 · 22.5K citations · Full text

Minimap2: pairwise alignment for nucleotide sequences

Heng Li · Bioinformatics · 2018 · 15.5K citations · Full text

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim, Joseph M. Paggi, Chanhee Park et al. · Nature Biotechnology · 2019 · 14.5K citations · Full text

Chromatin, Genetics, Genome Structure +6