Known isoform quantification software tools | RNA sequencing data analysis
Transcript identification and the quantification of gene expression have been distinct core activities in molecular biology ever since the discovery of RNA’s role as the key intermediate between the genome and the proteome. Scientists plan experiments and adopt different analysis strategies depending on the organism being studied and their research goals. For example, if a genome sequence is available for the studied organism, it should be possible to identify transcripts by mapping RNA-seq reads onto the genome.
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.
Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks assembles individual transcripts from RNA-seq reads that have been aligned to the genome. This software is able to infer the splicing structure of each gene because reads from multiple splice variants for a given gene can be found in a sample. Quantification of transcript abundances is also possible by preferring a reference annotation to assembling the reads.
Enables users to work with high-throughput sequencing data. HTSeq is a program that simplifies development of scripts for processing and analyzing high-throughput sequencing (HTS) data. It contains parsers for common file formats for a variety of types of input data and is suitable as a general platform for a diverse range of tasks.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Integrates workflow technology and in-built access to bioinformatics resources including remote data warehouses and tools. Galaxy permits users without programming skills to conduct computational analysis through the Web. It builds a succession of tools to perform multistep studies and is able to conserve the complete provenance of each analysis step. This platform offers drag and drop functionalities to ease the construction of workflows.
A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.
A program to enable the visualisation and analysis of mapped sequence data. SeqMonk was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are: (i) Import of mapped data from mapped data (BAM/SAM/bowtie etc), (ii) Creation of data groups for visualisation and analysis, (iii) Visualisation of mapped regions against an annotated genom, (iv) Flexible quantitation of the mapped data to allow comparisons between data sets, (v) Statistical analysis of data to find regions of interest and (vi) Creation of reports containing data and genome annotation.