Synima: a Synteny imaging tool for annotated genome assemblies
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-w...2125 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succint measure of quality at...reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly. We accomplish this...a quality score for every position in a genome a...2119 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
...h-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison w...Ades and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handl...2110 days ago
pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig bed (many options) bedgraph links (represented as arcs) Hi-C matrices (if HiCExplorer is installed)2115 days ago
AMStat: display statistics of large sequence files from next generation sequencing projects
SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation se...of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart...2114 days ago
2114 days ago
Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
...ol for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the post...rg/content/early/2017/08/09/173872 It uses the pyPaSWAS framework for sequence alignment (https://github.com...2112 days ago
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
...can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average...uld download and run this program directly. Or you could send us the genome sequence by email. Then we will do the...2110 days ago
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
NovoGraph: building whole genome graphs from long-read-based de novo...cally novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide...a proof of principle by creating a genome graph of seven ethnically-diver...2109 days ago
SISRS: Site Identification from Short Read Sequences
Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.2096 days ago