UHTS

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This page was reproduced and slightly edited from this one [1], written by people at the Netherlands Bioinformatics Centre [2]

Vendors sequencers

Category Source
Hardware vendor Illumina
Hardware vendor Pacific BioSciences
Hardware vendor Roche
Hardware vendor Helicos
Hardware vendor Applied Biosystems

Software

Category Package Description
Viewer EagleView genome viewer EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations.
Alignment MUMmerGPU MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.
Methylation Batman Bayesian tool for methylation analysis (Batman)—for analyzing methylated DNA immunoprecipitation (MeDIP) profiles
Base-calling Alta-Cyclic Alta-Cyclic is a novel Illumina Genome-Analyzer (Solexa) base caller. Alta Cyclic Features: Longer Reads, More Accurate Reads (compared to Solexa's default base caller), Reduces systematic bias towrsd a certain nucleotide in later cycles. On a GAII platform, Alta Cyclic was able to provide a large amount of useful reads after 78 cycles.
Enrichment/peak calling FindPeaks 3.1 Findpeaks was developed to perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest.
Assembly (de novo) ALLPATHS De novo assembly of whole-genome shotgun microreads.
Assembly (de novo) SHARCGS SHARCGS is a suitable tool for fully exploiting novel sequencing technologies by assembling sequence contigs de novo with high confidence and by outperforming existing assembly algorithms in terms of speed and accuracy. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics.
Assembly (de novo) Velvet Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).
Assembly (de novo) EDENA De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Made by Hernandez D et al.
Assembly SSAKE The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. SSAKE is designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux.
Alignment qpalma QPalma is an alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454. QPalma aligns short reads to the genomic sequences in an optimal way according to its underlying algorithm and trained parameters. It creates an alignment using dynamic programming (written in C++), and returns the alignment in a psl like format. The algorithms computes optimal local alignments, so if no alignment has been found it is because no alignment got a sufficiently high alignment score.
Alignment SOAP SOAP (Short Oligonucleotide Alignment Program) is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets. Author is Ruiqiang Li at the Beijing Genomics Institute. C++ for Unix.
Websites Galaxy
Blogs SeqAnswers
Integrated solutions CLCbio Genomics Workbench de novo and reference assembly of Sanger, 454, Solexa, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, browser and other features. Runs on Windows, Mac OS X and Linux.
Integrated solutions NextGENe de novo and reference assembly of Illumina and SOLiD data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly. Requires Win or MacOS.
Integrated solutions SeqMan Genome Analyser Software for Next Generation sequence assembly of Illumina, 454 Life Sciences and Sanger data integrating with Lasergene Sequence Analysis software for additional analysis and visualization capabilities. Can use a hybrid templated/de novo approach. Early release commercial software. Compatible with Windows® XP X64 and Mac OS X 10.4.
Alignment ELAND Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.
Assembly EULER Short read assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research).
Alignment Exonerate Various forms of alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.
Alignment & Mapping GMAP GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences. Developed by Thomas Wu and Colin Watanabe at Genentec. C/Perl for Unix.
Aligment & Assembly MOSAIK Reference guided aligner/assembler. Written by Michael Strömberg at Boston College.
Alignment & Mapping MAQ Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. Written by Heng Li from the Sanger Centre.
Alignment MUMmer MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Version 3.0 was developed by Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L Salzberg - most of whom are at The Institute for Genomic Research in Maryland, USA. POSIX OS required.
Alignment Novocraft Tools for reference alignment of paired-end and single-end Illumina reads. Uses a Needleman-Wunsch algorithm. Available free for evaluation, educational use and for use on open not-for-profit projects. Requires Linux or Mac OS X.
Assembly RMAP Assembles 20 - 64 bp Solexa reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.
Alignment SeqMap Works like ELand, can do 3 or more bp mismatches and also INDELs. Written by Hui Jiang from the Wong lab at Stanford. Builds available for most OS's.
Assembly SHRiMP Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. Works with data in letterspace (Roche, Illumina), colourspace (AB) and Helicos space.
Alignment SSAHA SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a tool for rapidly finding near exact matches in DNA or protein databases using a hash table. Developed at the Sanger Centre by Zemin Ning, Anthony Cox and James Mullikin. C++ for Linux/Alpha.
Alignment SXOligoSearch SXOligoSearch is a commercial platform offered by the Malaysian based Synamatix. Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent.
Assembly (de novo) MIRA2 MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.
Assembly (de novo) VCAKE De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.
SNP/Indel Discovery ssahaSNP ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac
SNP/Indel Discovery PolyBayesShort A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32.
SNP/Indel Discovery PyroBayes PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College.
Integrated solutions STADEN Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here
Viewer XMatchView A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux.
Integrated solutions SAM Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux.
Enrichment/peak calling CHiPSeq From Science Johnson, 2007
RNAseq ERANGE ERANGE is a Python package for doing RNA-seq and ChIP-seq (hence the "dual-use"), and is a descendant of the ChIPSeq mini peak finder (Johnson, 2007). In particular, the RNAseq analysis uses some of the very same code to access Cistematic. Version 2.0 is the first released in the wild and is "Bed"-centric. In particular, it is not optimized for speed!
Methylation BS-Seq The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.
Mapping gnumap he Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.
Mapping ZOOM ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority.
Assembly & Chromosome walking Tracembler Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations.
Enrichment/peak calling sissrs Produce a list of peakmaxima from aligned positions.
Assembly SHRAP The source code will be made available individually upon request. "However, note that we do not have a tool that can be used on real 454 sequence data in a production setting."
Alignment Phred Phrap Consed Cross_match The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. Phrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap.
Chromatine Profiling ChromaSig An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.
Integrated solutions Shore Analysis suite for Illumina short read data.
Mapping GenomeMapper Short read mapping tool.
Base-calling & Analysis Rolexa Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.
Integrated solutions SolexaTools SolexaTools is a project to create a tool set to work with a Solexa genome sequencer. It includes multiple components including a LIMS system, pipeline and other tools to support end-users and researchers setting up a Solexa environment.
ChIPseq QuEST QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).
Mapping SOCS SOCS is a program designed for efficient mapping of ABI SOLiD sequence data (Short Oligonucleotides in Color Space) to a reference genome with concurrent sequence census and SNP discovery functions.
Alignment BOWTIE Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: 1.3 GB for the human genome. It supports alignment policies equivalent to Maq and SOAP but is much faster: about 35x faster than Maq and over 350x faster than SOAP when aligning to the human genome.
Analysis CARPET Collection of Automated Routine Programs for Easy Tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs.
Assembly CABOG Celera Assembler is scientific software for DNA research. CA is a 'whole genome shotgun sequence assembler' -- it reconstructs long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage, and heterogeneous read lengths (pubmed).
ChIPseq / ChIP-chip PASS "..Motivated by the Poisson clumping heuristic, we propose an accurate and efficient method for evaluating statistical significance in genome-wide ChIP-chip tiling arrays. The method works accurately for any large number of multiple comparisons, and the computational cost for evaluating p-values does not increase with the total number of tests..." pubmed
ChIPseq / ChIP-chip CATCH CATCH is an tool for exploring patterns in ChIP profiling data. The CATCH algorithm performs a hierachical clustering of the profile patterns with an exhaustive alignment at each step. The algorithm has a user-friendly graphical interface that makes it easy for you to browse your results.
Misc DNAzip A series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment. pubmed
Integrated solutions CisGenome An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
Tiling-array analysis TiMat2 TiMAT2 contains tools for low and high level genomic tiling microarray analysis using the Affymetrix, NimbleGen, and Agilent platforms. It is designed for processing single and multi chip data sets from ChIP-Chip, RNA difference, and aCGH experiments.
microRNA CleaveLand A pipeline for using degradome data to find cleaved small RNA targets.
Alignment PECAN "..method of probabilistic consistency alignment and make it practical for the alignment of large genomic sequences. In so doing we develop a set of new technical methods, combined in a framework we term 'sequence progressive alignment', because it allows us to iteratively compute an alignment by passing over the input sequences from left to right. The result is that we massively decrease the memory consumption of the program relative to a naive implementation. The general engineering of the challenges faced in scaling such a computationally intensive process offer valuable lessons for planning related large-scale sequence analysis algorithms. We also further show the strong performance of Pecan using an extended analysis of ancient repeat alignments. Pecan is now one of the default alignment programs that has and is being used by a number of whole genome comparative genomic projects." pubmed
Assembly SHORTY "..Our assembler SHORTY is targetted for de novo assembly of microreads with mate pair information and sequencing errors. SHORTY has some novel approach and features in addressing the short read assembly problem.."
Assembly ABySS "ABySS is a de novo sequence assembler that is designed for very short reads. The single-processor version is useful for assembling genomes up to 40-50 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes."
Alignment PASS "PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of "seed" words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other." pubmed
ChIPSeq NPS "..Our method provides an effective framework for studying nucleosome positioning and epigenetic marks in mammalian genomes..." pubmed
Assembly Consensus SeqCons is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.
ChIPseq MACS Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Assembly Scheibye-Alsing et al A comprehensive overview of the current publicly available sequence assembly programs. pubmed
Transcript seq FrameDP Sensitive peptide detection on noisy matured sequences. A self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.
Enrichment/Peakcalling PeakSeq PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. A methodology for identifying punctate binding sites in ChIP-Seq experiments based on their characteristics. publication
Mapping SOCS SOCS is a program designed for efficient mapping of ABI SOLiD sequence data (Short Oligonucleotides in Color Space) to a reference genome with concurrent sequence census and mismatch identification functions.


Further reading

  • Accurate whole human genome sequencing using reversible terminator chemistry, Nature 456, 53-59 doi:10.1038/nature07517 [3]