BEDOPS v2.4.2 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale geno...
caspo combines BioASP and CellNOpt to provide an easy to use software for learning Protein Signaling Logic Models from a Prior Knowledge Network in .sif format and a phospho-proteomics dataset in MIDAS format.
Cassiopee is an index and search tool and library for bioinformatics (could be used for others but provides additional stuff usefull in sequence analysis). It is a complete rewrite of the ruby Cassiopee gem. It scan an input genomic sequence (dna/rna/protein) and search for a subsequenc...
Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, th...
Reporting server to collect SGE statistics Installed on arco vm. Uses iReport for report creation Data are uploaded with a local script made with Talend Studio
If you need to submit numerous job commands via qsub in the cluster, you can use the joborganizer tool. JobOrganizer is a utility tool we developped to submit a list of commands as jobs, while limiting the number of simultaneous jobs. This eases the way to submit numerous jobs without q...
KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer le...
miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center.
A tool that evaluates the accuracy of a genome assembly using mapped paired end reads. REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipelin...
Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based up...