VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
find the resources we provide here useful in getting you set up to analyse and interpret your data. To reference VESPA: https://peerj.com/preprints/1895/ Documentation is now hosted on ReadTheDocs1776 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package repre...1762 days ago
Cactus: a reference-free whole-genome multiple alignment program
...s each), you should expect Cactus to use approximately 120 CPU-days of compute per genome, with about 120 GB of RAM used at peak. The requirements scale roughly quadratically, so ali...1725 days ago
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Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
...s enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a si...1710 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
...typically results in improved contig N50 when compared to current state of the art methods. For smaller vertebrate genomes (~1 Gbp) chromosome scale assemblies can be achieved wi...1149 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both s...1398 days ago
pggb: the pangenome graph builder
...es into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local...1326 days ago
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