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ABySS +"ABySS is a de novo sequence assembler tha "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." is capable of assembling larger genomes."
ALLPATHS +De novo assembly of whole-genome shotgun microreads.
AMOS +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.
Alta-Cyclic +Alta-Cyclic is a novel Illumina Genome-Ana 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. ge amount of useful reads after 78 cycles.


BOWTIE +Bowtie is an ultrafast, memory-efficient s 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. an SOAP when aligning to the human genome.
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.
Batman +Bayesian tool for methylation analysis (Batman)—for analyzing methylated DNA immunoprecipitation (MeDIP) profiles


CABOG +Celera Assembler is scientific software fo 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). , and heterogeneous read lengths (pubmed).
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.
CATCH +CATCH is an tool for exploring patterns in 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. es it easy for you to browse your results.
CHiPSeq +From Science Johnson, 2007
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.
CNVseq +CNV-seq, a method to detect copy number variation using high-throughput sequencing. pubmed
ChIPmeta +In this work, hierarchical hidden Markov m 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 rces or a simple merger of the two. pubmed
ChromaSig +An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.
CisGenome +An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
CleaveLand +A pipeline for using degradome data to find cleaved small RNA targets.
CloudBurst +CloudBurst is a new parallel read-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 ution using multiple compute nodes. pubmed
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.


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


EDENA +De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Made by Hernandez D et al.
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.
ERANGE +ERANGE is a Python package for doing RNA-s 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! particular, it is not optimized for speed!
EULER +Short read assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research).
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.
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