REAPR: a universal tool for genome assembly evaluation
REAPR is a tool that evaluates the acc...using mapped paired end reads, without the use of...k incorrect scaffolds and flag other err...mbly based on the error calls. The software requires as input an...ailable, REAPR can combine this with the larg...se of the assembly. http://www.sanger.ac...2969 days ago
Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
Smash is a completely alignment-free...alise genomic rearrangements. The detection is based on con...ash outputs a SVG image, with an ideogramoutput architecture, where the patterns are represented with several HSV values ...ince that the main aim of the research...2949 days ago
RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
The RAST (Rapid Annotation using Subsyste...genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with...e. In this paper, we describe the RAST tool kit (RASTtk), a mod...version of RAST that enables researchers to build custom annot...2948 days ago
YASS :: genomic similarity search tool
...ise alignments). Like most of the heurist...ntial similarity regions, and then tri...ts, as non-coding DNA/RNA. Another simple, but interesting feat...ing different scoring schemes with bit-score and E-value evaluated according to the se...ion) post-processing step to group gap...2943 days ago
Painless package development for R
Devtools makes package development a breeze: it works with R’s existing conventions...ding efficient tools to support the cycle of package development. With devtools, developing a package becomes so easy that it will be...o check out: devtools Google Group – https://groups.go...2942 days ago
2935 days ago
SATSUMA : Highly sensitive whole-genome synteny alignments.
...mes, computes alignments, and then keeps only the parts...on multi-core architectures. The run-time for aligning two bir...be downloaded from the Broad Institute's web site. An incompl...f questions and answers (yes, these.... If you use Satsuma in your research, please cite: Grabherr, M. G.,...2932 days ago
RCircos: an R package for Circos 2D track plots
RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R...ines for presenting large-scale multi-sample genomic research...2925 days ago
Bpipe - a tool for running and managing bioinformatics pipelines
Bpipe provides a platform for running big bioinformatics jobs that consist of a series of pr...New! Bpipe 0.9.9 released! Download latest, all Documentation Mailing List (Google Group)...2923 days ago
2901 days ago