2728 days ago
Standardized velvet assembly report
...ments: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable"))...2717 days ago
GARM:Genome Assembly, Reconciliation and Merging
...mplemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on D...2707 days ago
2667 days ago
2621 days ago
Pacbio Long Reads Compatible Software and Tools
The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open sourc...2621 days ago
2591 days ago
2525 days ago
CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
...gnment Search Tool (BLAST) has revolutionized the field of bioinformatics, and is currently implemented in all free and commercial bioinformatics packages. However, with the advent of...2489 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...en-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling...2362 days ago