Hapsembler: An Assembler for Highly Polymorphic Genomes
Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/2228 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g....2225 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...th the intent of: Reducing time in analysis and increasing accuracy of result...le subsets which can then be assembled quickly and efficiently in parallel. Appl...esearcher wishes to de novo assemble specific content and a set of semi-sim...2163 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an...2092 days ago
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HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in t...mplishes this by: Learning locus-specific PCR stutter models using an EM algorithm Mining candidate STR alleles fro...den Markov model to align reads to candidate alleles while accounting for...1938 days ago
HumCFS: a database of fragile sites in human chromosomes
Fragile sites are specific chromosomal region that exhibit an increased frequency...suggests their involvement in human pathologies and they have been recognized as...r integration of exogenous oncogenic DNA viruses and hotspots for chromosom...1893 days ago
Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
...RNA), miRNAs, repeat regions, and transposable elements; each a...rectly set an annotation to a specific state, choosing from the...story’ display. Adding and updating PubMed IDs will prompt us...page. Help page with Apollo specific content is available....1853 days ago
Retrieving Taxonomic Information with R
...ful package taxize. Nevertheless, taxonomic information retrieval has been customized for the myTAI standard and for organism specific information retrieval. Specifically, the taxonomy() ...1764 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or ch...the chromosome plot.Each chromosome is composed of loci(representing a specific range determined based on chr...1754 days ago