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 ...
accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Both single and paired ends are supported.
EpiGRAPH enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest (e.g. experimentally mapped enhancers, hotspots of epigenetic regulation or sites exh...
inGAP is an integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.
Integrated Next-gen Genome Analysis Platform run with /biosoft/inGAP_linux64/inGAP
de novo genome assembly is now a challenge because of the overwhelming amount of data produced by sequencers. Ray assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2 -- a message passing inferface standard.
Ray is a paralleled computer-contr...
Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality.
Quality Value ...
Identifies genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligner...
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly
Omixon Target Standard, Target HLA and Target Pro are designed to help clinical, diagnostic and research labs to efficiently get the maximum accuracy and precision from their targeted NGS data.
ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. ChIPMunk identifies the strong motif with the maximum Kullback Discrete Information Content in a given set of DNA sequences. *NEW URL* http://autosome.ru/ChIPMunk
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.