2384 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 ba...a obtained by differential coverage binning of multiple metagenomes Mads...2384 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 data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulf...1865 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 Instit...2383 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 Assemb...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...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 struct...2363 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 th...2377 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a...2045 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)...2375 days ago