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Items: 7


Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data.

Lima L, Marchet C, Caboche S, Da Silva C, Istace B, Aury JM, Touzet H, Chikhi R.

Brief Bioinform. 2019 Jun 24. pii: bbz058. doi: 10.1093/bib/bbz058. [Epub ahead of print]


De novo clustering of long reads by gene from transcriptomics data.

Marchet C, Lecompte L, Silva CD, Cruaud C, Aury JM, Nicolas J, Peterlongo P.

Nucleic Acids Res. 2019 Jan 10;47(1):e2. doi: 10.1093/nar/gky834.


A de novo approach to disentangle partner identity and function in holobiont systems.

Meng A, Marchet C, Corre E, Peterlongo P, Alberti A, Da Silva C, Wincker P, Pelletier E, Probert I, Decelle J, Le Crom S, Not F, Bittner L.

Microbiome. 2018 Jun 9;6(1):105. doi: 10.1186/s40168-018-0481-9.


Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data.

Benoit-Pilven C, Marchet C, Chautard E, Lima L, Lambert MP, Sacomoto G, Rey A, Cologne A, Terrone S, Dulaurier L, Claude JB, Bourgeois CF, Auboeuf D, Lacroix V.

Sci Rep. 2018 Mar 9;8(1):4307. doi: 10.1038/s41598-018-21770-7.


Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

Lima L, Sinaimeri B, Sacomoto G, Lopez-Maestre H, Marchet C, Miele V, Sagot MF, Lacroix V.

Algorithms Mol Biol. 2017 Feb 22;12:2. doi: 10.1186/s13015-017-0091-2. eCollection 2017.


SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.

Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, Filali AE, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V.

Nucleic Acids Res. 2016 Nov 2;44(19):e148. Epub 2016 Jul 25.


Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.

Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P.

Gigascience. 2016 Feb 11;5:9. doi: 10.1186/s13742-015-0105-2. eCollection 2016.

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