List of RNA-Seq bioinformatics tools #源自维基百科

Quality control and filtering data

Quality assessment is essential to the overall comprehension of RNA-Seq, as well to guarantee that data are in the right format and suitable for the next analyses. Often, is necessary to filter data, removing low quality sequences, linkers, overrepresented sequences or noise to assure a coherent final result.

cutadapt cutadapt removes adapter sequences from next-generation sequencing data (Illumina, SOLiD and 454). It is used especially when the read length of the sequencing machine is longer than the sequenced molecule, like the microRNA case.

FastQC FastQC is a quality control tool for high-throughput sequence data (Babraham Institute) and is developed in Java. Import of data is possible from FastQ files, BAM or SAM format. This tool provides an overview to inform about problematic areas, summary graphs and tables to rapid assessment of data. Results are presented in HTML permanent reports. FastQC can be run as a stand alone application or it can be integrated into a larger pipeline solution. See also seqanswers/FastQC.

FASTX FASTX Toolkit is a set of command line tools to manipulate reads in files FASTA or FASTQformat. These commands make possible preprocess the files before mapping with tools like Bowtie. Some of the tasks allowed are: conversion from FASTQ to FASTA format, information about statistics of quality, removing sequencing adapters, filtering and cutting sequences based on quality or conversion DNA/RNA.

HTSeq HTSeq.

htSeqTools htSeqTools is a Bioconductor package able to perform quality control, processing of data and visualization. htSeqTools makes possible visualize sample correlations, to remove over-amplification artifacts, to assess enrichment efficiency, to correct strand bias and visualize hits.

RNA-SeQC RNA-SeQC is a tool with application in experiment design, process optimization and quality control before computational analysis. Essentially, provides three types of quality control: read counts (such as duplicate reads, mapped reads and mapped unique reads, rRNA reads, transcript-annotated reads, strand specificity), coverage (like mean coverage, mean coefficient of variation, 5’/3’ coverage, gaps in coverage, GC bias) and expression correlation (the tool provides RPKM-based estimation of expression levels). RNA-SeQC is implemented in Java and is not required installation, however can be run using the GenePattern web interface. The input could be one or more BAM files. HTML reports are generated as output.

RSeQC RSeQC analyzes diverse aspects of RNA-Seq experiments: sequence quality, sequencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. The input can be SAM, BAM, FASTA, BED files or Chromosome size file (two-column, plain text file). Visualization can be performed by genome browsers like UCSC, IGB and IGV. However, R scripts can also be used to visualization.

SAMStat SAMStat identifies problems and reports several statistics at different phases of the process. This tool evaluates unmapped, poorly and accurately mapped sequences independently to infer possible causes of poor mapping.

ShortRead ShortRead is a package provided in the R (programming language)/BioConductor environments and allows input, manipulation, quality assessment and output of next-generation sequencing data. This tool makes possible manipulation of data, such as filter solutions to remove reads based on predefined criteria. ShortRead could be complemented with several Bioconductor packages to further analysis and visualization solutions (BioStrings,BSgenome,IRanges, and so on). See also seqanswers/ShortRead.

TrimmomaticTrimmomatic performs trimming for Illumina platforms and works with FASTQ reads (single or pair-ended). Some of the tasks executed are: cut adapters, cut bases in optional positions based on quality thresholds, cut reads to a specific length, converts quality scores to Phred-33/64.

Alignment Tools

After control assessment, the first step of RNA-Seq analysis involves alignment(RNA-Seq alignment)of the sequenced reads to a reference genome (if available) or to a transcriptome database. See List of sequence alignment software and HTS Mappers.

Short (Unspliced) aligners

Short aligners are able to align continuous reads (not containing gaps result of splicing) to a genome of reference. Basically, there are two types: 

1) based on the Burrows-Wheeler transform method such as Bowtie and BWA

2) based on Seed-extend methods,Needleman-WunschorSmith-Waterman algorithms. 

The first group (Bowtie and BWA) is many times faster, however some tools of the second group, despite the time spent tend to be more sensitive, generating more reads correctly aligned.

BFAST BFAST aligns short reads to reference sequences and presents particular sensitivity towards errors, SNPs, insertions and deletions. BFAST works with the Smith-Waterman algorithm. See also seqanwers/BFAST.

Bowtie Bowtie is a fast short aligner using an algorithm based on the Burrows-Wheeler transform and the FM-index. Bowtie tolerates a small number of mismatches. See also seqanswers/Bowtie.

Burrows-Wheeler Aligner (