Mapping and Assembly

This section contains links to mapping data, contig assembly, and genome resources used by many genome sequencing projects.

Found 33 links

Displaying 15 links

eBioinformaticsResource Content

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This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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EGassemblerTool Content

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EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.

This content is being maintained by amasoudin.

FPCTool Content

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FPC is a tool to assemble contigs from a set of clones and their restriction fragments.

Genome Centres and DatabasesResource Content

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Genome centers and databases listed by organism.

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HapEditTool Content

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HapEdit is a tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.

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MagicViewerTool Content

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MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.

MGIPTool Content

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The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

MIRATool Content

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The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For EST transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof.

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NCBI Clone RegistryDatabase Content

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A database that integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information.

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OriDBDatabase Content

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DNA origin of replication database: contains genome-wide mapping studies. Databases available for yeast Saccharomyces cervisiae and S. pombe.

PeakSeqTool Content

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PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

Phred/Phrap/Consed SystemTool Content

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UNIX-based, base-calling, sequence assembly and finishing tools used by most genome sequence centres; free for non-commercial use.

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