BOL

www.sanger.ac.uk - PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an...

github.com - Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...

New SPAdes 3.15.0.0. announced by the SPADes team

metagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...

github.com - The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any...

http://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...

mugsy.sourceforge.net - Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee....

DOWNLOAD LINK: https://github.com/BioInf-Wuerzburg/proovread/raw/master/util/blasr-1.3.1/blasr I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error: fail to open file './temporarySam' [bwa_aln_core] write to the...

gfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...

github.com - Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included...