ATGC: NGS - Next Generation Sequencing

Next Generation Sequencing (NGS)

Softwares and libraries

The ATGC platform is backed up by research teams in bioinformatics and genomics. Research endeavors deliver usable programs, software, methodological protocols, and reusable program libraries for further developments of HTS bioinformatic tool. An objective of the HTS platform is to disseminate these productions for improving HTS data analysis in general.

Softwares and programs

MPSCAN: exactly mapping short reads on a reference genome without an index (no genome preprocessing is required)
PermutMatrix: clustering and reordering of expression level data

Reusable libraries

Gk-arrays: provide a data structure to index large read sets of fixed or variable length

Related publications

Methodology:

Gk-arrays: Querying large read sets in main memory: a versatile data structure

Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Leonard, Therese Commes and Eric Rivals

BMC Bioinformatics, 12:242, doi:10.1186/1471-2105-12-242; 2011.
Exact Search Algorithms for Biological Sequences

E. Rivals, L. Salmela, J. Tarhio

Algorithms in Computational Molecular Biology: Techniques , Approaches and Applications, pages 1-22, ISBN : 978-0470505199, Wiley Series in Bioinformatics, Wiley, 2010.
Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

N. Philippe*, A. Boureux*, L. Bréhèlin, J. Tarhio, T. Commes, E. Rivals

Nucleic Acids Research (NAR) Vol. 37, No. 15 e104, doi:10.1093/nar/gkp492; 2009.
MPSCAN: fast localisation of multiple reads in genomes

E. Rivals, L. Salmela, P. Kiiskinen, P. Kalsi, J. Tarhio

Proc. 9th Workshop on Algorithms in Bioinformatics
Lecture Notes in BioInformatics (LNBI), Springer-Verlag, Vol. 5724, p. 246-260, 2009.
Transcriptome Annotation using Tandem SAGE Tags

E. Rivals*, A. Boureux*, M. Lejeune, F. Ottones, O. Pecharroman Pérez, J. Tarhio, F. Pierrat, F. Ruffle, T. Commes, J. Marti

Nucleic Acids Research (NAR), Vol. 35(17):e108, http://dx.doi.org/10.1093/nar/gkm495

Cancer related abstracts:

RNA sequencing, conservation and non-coding RNA

Philippe, N; Ruffle, F; Bou-Samra E; Boureux A; Commes, T; Rivals, E

BULLETIN DU CANCER, 97: S44-S44 Suppl. 4 OCT 2010. ISSN: 0007-4551
Estimation of sequence errors and capacity of genomic annotation in transcriptomic and dna-protein interaction assays based on next generation sequencers

N. Philippe, A. Boureux, L. Bréhèlin, J. Tarhio, T. Commes, E. Rivals

CELLULAR ONCOLOGY, 31 (2): 145-146 2009. ISSN: 1570-5870
New approaches based on high throughput sequencing and bioinformatics to study the transcriptomes of leukemic stem cells

A. Boureux*, L. Bréhèlin, E. Rivals, T. Commes

BULLETIN DU CANCER, 96: S33-S33 Sp. Iss. 3 OCT 2009. ISSN: 0007-4551