2380 days ago
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 sequences of rare, uncultured b...obtained by differential coverage binning of multiple metagenomes Mads...2380 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 simplify the analysis of NGS...ata. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulfi...1861 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 sequencing data developed on Facul...ectrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institu...2379 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation...tegrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the gr...sp;From de Bruijn Graphs to Rectangle Graphs for Genome Assembl...2378 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 H...2378 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 structu...2359 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool eva...Reading a pre-existing reference genome from one or more FASTA files...., generating an artificial reference genome based on input parameters (le...te. Applying alignment tools to the genome and the...2373 days ago
LRCstats: Long Read Correction Statistics
LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted...ncorrected long reads (uLR) and the corresponding sequences in the reference genome (Ref) a...2371 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the impl...(embl format) can be automatically loaded into the freely available Artemis genome viewer....2368 days ago