Summary WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order…

Overview In a nutshell, LoRDEC is a program for error correcting long sequencing reads using short reads. It implements a hybrid correction approach. It uses little memory and is very efficient. Most importantly it scales up to process very large data sets. It can be applied to long reads obtained with either Pacific Biosciences SMRT…

Overview LoRMA is an error correction program for long reads, which are sequences obtained using the third generation of sequencing technologies (3GS), either with Oxford Nanopore technology or with Pacific Biosciences technology. LoRMA is a so-called self-correction software, as opposed to e.g. LoRDEC that is a hybrid error correction tool. This means that LoRMA uses…

Introduction and context In the Bioinformatics team of the LIRMM (CNRS & Univ. Montpellier), we develop a series of tools for metagenomics / metabarcoding analysis. Our tools exploit phylo-k-mers (which are k-mers combined with phylogenetic information) computed for an input set of reference sequences and their phylogeny. The phylo-k-mers are computed and indexed with IPK,…

Overview Overview: In the protein coding sequences of a species, the 61 possible codons of the genetic code are not equally distributed. This observation is referred to as the Codon Usage Bias (CUB) of a species. Several measures have been proposed to quantify the CUB using the frequencies of codons in all RNA coding sequences…