Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectatio

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 program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. I

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

A tool for transcript expression quantification from RNA-seq data

A tool for transcript expression quantification from RNA-seq data

Ultrafast universal RNA-seq aligner. Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately

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

Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which a

An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with