Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies...s would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely di...1972 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenaz...1854 days ago
Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets
Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute...act: claire dot lemaitre at inria dot fr Simka and SimkaMin are comparative metagenomics method dedicated to NGS datas...1807 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRI...n Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium d...1762 days ago
Seq: A high-performance, Pythonic language for bioinformatics
Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host...features and optimizations, Seq makes writing high-performance genomics software as easy as writing P...1667 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly u...1652 days ago
LibsDyogen: Libibrary for comparative genomics
Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications. Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in vertebrates. http://www.ibens.ens.fr/?rubrique43&lang=fr1635 days ago
1604 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enum...1601 days ago
Nucleus: Python and C++ code for reading and writing genomics data.
Nucleus is a library of Python and C++ code designed to make...it easy to read, write and analyze data in common genomics file formats like SAM and VCF...sorFlow machine learning framework, as anywhere a genomics file is consumed or produced,...1596 days ago