Tool Library list page for genomics topic with tag 'Transcriptomics'
A simple way to screen a library of short reads against a set of reference libraries. Its most common use is as part of a QC pipeline to confirm that a library comes from the expected source, and to help identify any sources of contamination.
A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Ultrafast universal RNA-seq aligner. Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately aligning long (several kilobases) reads that are emerging from the third-generation sequencing technologies.
Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.