mojolicious: a next generation web framework for the Perl programming language.
...-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed) Fresh code...2298 days ago
2291 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...n extra repeat classification and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a polisher module, which produces the final ass...2186 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-...2147 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
...h the positions, sequence, and flanking base pairs of each such structural feature. The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts f...2168 days ago
KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment
...ver for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it acc...out pathways, diseases, and Gene Ontology. For Enrichment module, it can accept either gene li...2018 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site o...1921 days ago
Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo: https://vgteam.github.io/sequenceTubeMap/1510 days ago
Juicebox: Visualization and analysis software for Hi-C data
...s and the Juicebox jar files. Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab...1529 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structu...1442 days ago