2764 days ago
BIMA V3: an aligner customized for mate pair library sequencing
Summary: Mate pair library sequencing is an effective and economical method for de...d chromosomal abnormalities. Unfortunately, the mapp...presence of structural variant breakpoints within...bility: http://bioinformaticstools.mayo.edu/research/...2748 days ago
e-RGA: enhanced Reference Guided Assembly of Complex Genomes
Next Generation Sequencing has totally chang...incredibly low cost compared to Sanger sequencing. Despite this, s..., de novo, an organism sequenced with short reads, the results are still far from those achievable with long reads. In this paper, w...s to improve de novo assembly in the prese...2743 days ago
2020 days ago
2742 days ago
splitbam: splits a BAM by chromosomes
splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it...n '-e', add a mock pair of sam records to the empt...MUST contain __CHROM__ and end with ....(dir) tmp file directory -G (file) chrom-group fil...2672 days ago
2608 days ago
A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
PAGIT addresses the need for software to generat...tion. It is able to close gaps left open by the assembler in a draft genome, even when using the same data sets as used by the...y, onto the latest assembly. PAGIT bundles these sof...2599 days ago
CABOG: Celera Assembler with Best Overlap Graph
CABOG (Celera Assembler with Best Overl...ian. CABOG is an extension of the Celera...loped at Celera for the 2001 publication of the first draf...ams called genome assemblers. These programs exist to overcome.... Craig Venter, 2007). It was the firs...e reads from first-generation Sanger se...2596 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun...rom current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accu...matic tools under specific hypothesis, e.g. with or without s...2587 days ago