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GenNovation B.V.
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A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats
🗻 Fuji plot—a circos representation of multiple GWAS results— 🗻
Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Java library for nanopublications based on RDF4J
Hagfish - assess an assembly through creative use of coverage plots
VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerfu…
OmicsFusion is a web application which can perform univariate regression and a number of modern regression techniques and then ranks the predictors according to an importance criterion (mean rank o…
Tools for working with second gen assemblies, fasta sequences, etc
Repetitive motif detection by Assembly of Repetitive K-mers. RepARK is free for academic and non-profit use. By downloading you agree with the FLI-LICENSE included in the package.
A professional front-end template for building fast, robust, and adaptable web apps or sites.
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
Project directory for the analysis of ancient tomato DNA
RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux. These libraries provide usefull utilities for bioinformatics programming in C. This m…
RStudio is an integrated development environment (IDE) for R
Scripts for design of PCR-based Marker Assays from DNA sequence variant data, plus Galaxy xml files
Java library to automatically link a chebi compound/identifier to a metabolic pathway or genes from the tomato genome.
Breakpointer is a fast algorithm to locate breakpoints of structural variants from single-end reads produced by next-generation sequencing.
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
An ontology database for crops' traits with their variables
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses