TopHat is a fast splice junction mapper for RNA-Seq reads.
A fast splice junction mapper for RNA-seq reads that uses bowtie (see above)
s a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read al...
Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support ...
标签：RNA-Seq Alignment, RNA-Seq Quantitation, Alternative Splicing, Transcriptome, RNA-Seq
Sequence assembly software using traditional, next-gen, and third-gen techonologies. Subsequent analysis of the assembly, including SNP discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.
标签：Genomics, De-novo assembly, De novo transcriptome assembly,Whole Genome Resequencing, SNP discovery, InDel discovery,ChIP-Seq, RNA-Seq Alignment
GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program al...
We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the res...
Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations
Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to i...
We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (75 bp). MapSplice is not dependent...
Novoalign is a program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome.
Package for aligning short reads to reference genomes
a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence ...
Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of (~)11.4 million reads per hour.