RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex...n be performed. A typical application of RGFA is the edi...1581 days ago
2222 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82211 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of h...2203 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it b...2178 days ago
BEAP: Blast Extension and Assembly Program
The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or part...2169 days ago
2196 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just w...2196 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well...2183 days ago
2105 days ago