Bio2M

Address

BioInformatiques et BioMarqueurs INSERM U1183 IRMB - Institut de Médecine Regénérative et Biothérapie Hôpital Saint-Eloi 80, av. Augustin Fliche
43.624386, 3.868455

Attachment

Structure
Unit

Outlinks

homepage: [long name is missing in model]
legacy catalog: Try opening in it

Scientific Leaders

Commes Thérèse
Boureux Anthony

Technical Leaders

Boureux Anthony

Certificats

Team

Commes Thérèse
Guibert Benoit
Rufflé Florence
Boureux Anthony

Data

Kmerator

biotoolsID: kmerator
homepage: https://github.com/Transipedia/kmerator
last_update: June 24, 2022, 9:50 a.m.
more: ...

Description

Kmerator is a prototype tool designed for the prediction of specific k-mers (also called tags) from input sequences, considering a reference genome and an ENSEMBL-like transcriptome. From these specific k-mers, it also outputs their corresponding specific contigs which are sequences of consecutive k-mers (overlapping length between k-mers must be k-1, otherwise, it's a new contig). Kmerator first uses Jellyfish to create 2 requestable indexes from the reference genome and transcriptome, and second, decomposes your input transcript or gene sequences to count the occurences of each k-mer in the genome and transcriptome.

Domains of activity

Biologie

Description of expertise domains

The bioinformatic group involved specialists in text algorithm focusing on the design of new tools and structures for RNA-Seq analysis. We have created a new data structure capable of organizing reads for very quickly queries and developed a software (called CRAC) noticed by Nature as a competitor over existing softwares for the analysis of RNA-Seq data (CRAC, Star, …).

* Transcriptomics - RNA-Seq
* Kmers analysis
- [Transipedia](https://transipedia.fr)

Keywords

metatranscriptomics
Transcriptomics
Transcript and transcript variant analysis
Transcriptomics (RNA-seq)

Querying large read collections in main memory: a versatile data structure Philippe Nicolas, Salson Mikaël, Lecroq Thierry, Léonard Martine, Commes Thérèse, Rivals Eric. 2011, BMC Bioinformatics. 10.1186/1471-2105-12-242

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CRAC: an integrated approach to the analysis of RNA-seq reads Philippe Nicolas, Salson Mikaël, Commes Thérèse, Rivals Eric. 2013, Genome Biology. 10.1186/gb-2013-14-3-r30

Kmerator Suite: design of specific <i>k</i>-mer signatures and automatic metadata discovery in large RNA-seq datasets Riquier Sébastien, Bessiere Chloé, Guibert Benoit, Bouge Anne-Laure, Boureux Anthony, Ruffle Florence, Audoux Jérôme, Gilbert Nicolas, Xue Haoliang, Gautheret Daniel, Commes Thérèse. 2021, NAR Genomics and Bioinformatics. 10.1093/nargab/lqab058

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