Spliced read alignment software tools | RNA sequencing data analysis
Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events.
Aligns high-throughput long and short RNA-seq data to a reference genome using uncompressed suffix arrays. STAR is a standalone software capable of align reads in a continuous streaming mode. The application first run a seed search for then perform seed clustering and stitching. It is able to detect canonical junctions, non-canonical splices and chimeric transcripts and to map full-length RNA sequences.
Assists users in mapping reads to a reference genome. Subread offers a suite of programs for processing next-generation sequencing read data. This package includes Subread (an aligner), Subjunc (an aligner), Sublong (a long-read aligner), Subindel (a long indel detection program), featureCounts (a read quantification program), exactSNP (an SNP calling program) and other utility programs.
Uses as a splice-aware aligner for short and long reads. BBTools is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations than others. It has particularly outstanding performance with deletions, especially long ones, that other aligners cannot handle at all. It can output many different statistics files, such as an empirical read quality histogram, insert-size distribution, and genome coverage, with or without generating a sam file.
Executes alignments for single- and paired-end reads. GSNAP exploits probabilistic models or a database of known splice sites to identifies short and long-distance splicing in individual reads. This software uses a constrained search strategy for producing candidate genomic regions by combining position lists from oligomers across the entire read. The search procedure works at the oligomer level, which differs from the nucleotide-level backtracking procedures.
Performs gene and isoform level quantification from RNA-Seq data. RSEM is a software package that quantifies gene and isoform abundances from single-end (SE) or paired-end (PE) RNA-Seq data. The software enables visualization of its output through probabilistically-weighted read alignments and read depth plots. It does not require a reference genome and can be used for quantifying de novo transcriptome assemblies.
Allows users to handle RNA-sequencing pipeline based on the TopHat, Cufflinks and CummeRbund suite of software. Tuxedo is a program that enables assessment of alternative splicing (AS) inferred on fragments per kilobase per million (FPKM) values. It can assist researchers to detect genes and splicing variants and compare gene expression and transcripts under different conditions.
Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie. TopHat also analyzes the mapping results to identify splice junctions between exons. It can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. The tool combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes.