Recovery of complete genomes from metagenomes
This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome se...by differential coverage binning of multiple metagenomes Mads Albertsen, Philip...2385 days ago
snakepipes: A toolkit based on snakemake and python for analysis of NGS data
snakePipes are flexible and powerful workflows built using snakemake that...data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulfite Seq/WGBS (*Also...1866 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
Integration of the Ra assembler - a de novo DNA assembler for third generation seque...Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS)....2384 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementat...ate RGM in SPAdes. RGM can be run with other genome assemblers if they use the gr...rom de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes...2383 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 yields chromosome-...2383 days ago
GPOPSIM: a simulation tool for whole-genome genetic data
GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic...2364 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing sim...: Reading a pre-existing reference genome from one or more FASTA files....y, generating an artificial reference genome based on input parameters (le...ate. Applying alignment tools to the genome and the reads through a stand...2378 days ago
LRCstats: Long Read Correction Statistics
LRCstats is an open-source pipeline for benchmarking DNA long read correction algori...uncorrected long reads (uLR) and the corresponding sequences in the reference genome (Ref) are given in some sort...2376 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
Alien_hunter is an application for the prediction of putative Horizontal Gene Transf...ns (embl format) can be automatically loaded into the freely available Artemis genome viewer.2373 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https...2371 days ago