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Work in progress.

For previous software in the wiki, see: Software!

NGS Sandbox

Tabulate entries

Tag Homepage Description Notes
ABySS Assembly "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." None
ALLPATHS Assembly (de novo) De novo assembly of whole-genome shotgun microreads. None
AMOS Assembly The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler. None
Alta-Cyclic Base-calling 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. None
BOWTIE Alignment 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. None
BS-Seq Methylation 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. None
Batman Methylation Bayesian tool for methylation analysis (Batman)—for analyzing methylated DNA immunoprecipitation (MeDIP) profiles None
CABOG Assembly 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). None
CARPET Analysis 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. None
CATCH ChIPseq / ChIP-chip 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. None
CHiPSeq Enrichment/peak calling From Science Johnson, 2007 None
CLCbio Genomics Workbench Integrated solutions 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. None
CNVseq CNV CNV-seq, a method to detect copy number variation using high-throughput sequencing. pubmed None
ChIPmeta ChIPseq In this work, hierarchical hidden Markov model (HHMM) is proposed for combining data from ChIP-seq and ChIP-chip. In HHMM, inference results from individual HMMs in ChIP-seq and ChIP-chip experiments are summarized by a higher level HMM. Simulation studies show the advantage of HHMM when data from both technologies co-exist. Analysis of two well-studied transcription factors, NRSF and CTCF, also suggests that HHMM yields improved TFBS identification in comparison to analyses using individual data sources or a simple merger of the two. pubmed None
ChromaSig Chromatine Profiling An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. None
CisGenome Integrated solutions An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis None
CleaveLand microRNA A pipeline for using degradome data to find cleaved small RNA targets. None
CloudBurst Mapping CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. It is modeled after the short read mapping program RMAP, and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences. This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. pubmed None
Consensus Assembly 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. None
DNAzip Misc A series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment. pubmed None
EDENA Assembly (de novo) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Made by Hernandez D et al. None
ELAND Alignment 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. None
ERANGE RNAseq 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! None
EULER Assembly Short read assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research). None
EagleView genome viewer 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. None
Exonerate Alignment 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. None
FindPeaks 3.1 Enrichment/peak calling 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. None
FrameDP Transcript seq 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. None
Galaxy Websites None
GenomeMapper Mapping Short read mapping tool. None
Gnumap Mapping 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. None
HawkEye Viewer An Interactive Visual Analytics Tool for Genome Assemblies. None
LOCAS Assembly LOCAS low-coverage short-read assembler None
MACS ChIPseq 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. None
MAQ Alignment & Mapping 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. None
MEGAN Metagenome Metagenome Analysis Software - MEGAN (“MEtaGenome ANalyzer”) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. None
MIRA2 Assembly (de novo) 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. None
MOSAIK Alignment & Assembly Reference guided aligner/assembler. Written by Michael Strömberg at Boston College. None
MUMmerGPU Alignment 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. None
MapView Viewer Visualization of short reads alignment on desktop computer None
NPS ChIPSeq "..Our method provides an effective framework for studying nucleosome positioning and epigenetic marks in mammalian genomes..." pubmed None
NextGENe Integrated solutions 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. None
Novocraft Alignment 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. None
PASS ChIPseq / ChIP-chip "..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 None
PECAN Alignment "..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 None
PeakSeq Enrichment/Peakcalling 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 None
Phred Phrap Consed Cross match Alignment 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. None
Pindel Indel A pattern growth approach to detect break points of large deletions and medium sized insertions from pairedend short reads. None
PolyBayesShort SNP/Indel Discovery 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. None
PyroBayes SNP/Indel Discovery 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. None
… further results
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