MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to dete...2300 days ago
Recovery of complete genomes from metagenomes
...ains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome seq...bacteria obtained by differential coverage binning of multiple metagenomes Mads Albertsen, Philip...2349 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yiel...2348 days ago
HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how like...2328 days ago
HTTDB - Horizontally transferred transposable elements database
...ish genomic parasites. Despite their capacity for transposition inside genomes, they can frequently transpos...such discoveries have been boosted by the unprecedented amount of new genomes available. Despite the recogn...2322 days ago
karyoploteR: plot whole genomes with arbitrary data
karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and...1979 days ago
MUMmer4: A fast and versatile genome alignment system
...stic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to handle alignments of large genomes;2311 days ago
2299 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and suggests the fol...to GRCh38 or hg38, use the following: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_00000...1566 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
...m likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related...2280 days ago