snakepipes: A toolkit based on snakemake and python for analysis of NGS data
...ws built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulfite Seq/WGBS (*Also...1846 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
...embler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS)....2364 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific impl...grate RGM in SPAdes. RGM can be run with other genome assemblers if they use the gr...;From de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes...2364 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
...de 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-...2364 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 architectures. It provides flexible param...2344 days ago
Seal: SEquence ALignment evaluation suite
...including: Reading a pre-existing reference genome from one or more FASTA files....ernatively, generating an artificial reference genome based on input parameters (le...d indel rate. Applying alignment tools to the genome and the reads through a stand...2358 days ago
LRCstats: Long Read Correction Statistics
...(such as SimLoRD or PBSim) where the two-way alignments between the uncorrected long reads (uLR) and the corresponding sequences in the reference genome (Ref) are given in some sort...2356 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
...calization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.2353 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://git...2351 days ago
AliTV—interactive visualization of whole genome comparisons
AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annota...2351 days ago