1835 days ago
gEVAL: Genome Evaluation Browser
...ng potential solutions for these issues. This facilitates the improvement of overall assemblies to a “gold” standard for release as reference genomes1835 days ago
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 ReadTheDocs1831 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or s...1797 days ago
GffCompare: Program for processing GTF/GFF files
The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).1814 days ago
Cactus: a reference-free whole-genome multiple alignment program
Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substa...1780 days ago
1766 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...oodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft g...s into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this too...1704 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most...otype correspondence for each heterozygous variant called on a phased reference genome. Availability and Imp...1651 days ago
MGSE: Mapping-based Genome Size Estimation
...is COV file can be used by MGSE to calculate the coverage in provided reference regions and to calculate the...alues are subjected to the genome size estimation. Providing accurate reference regions is crucial for this g...1622 days ago