Author's posts

Paper CARNAC-LR published in NAR: “De novo clustering of long reads by gene from transcriptomics data”

Our paper “De novo clustering of long reads by gene from transcriptomics data” was published late October 2018 in NAR. It describes the CARNAC-LR tool developed by Camille Marchet

Permanent link to this article: https://team.inria.fr/genscale/paper-carnac-lr-published-in-nar-de-novo-clustering-of-long-reads-by-gene-from-transcriptomics-data/

Long Reads RNA-seq de novo clustering – preprint

De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets Preprint: biorxiv.org/content/early/ Tool: https://github.com/kamimrcht/CARNAC

Permanent link to this article: https://team.inria.fr/genscale/long-reads-rna-seq-de-novo-clustering-preprint/

discoSnp goes to RAD seq

We propose an adaptation of DiscoSnp for RadSeq data. Paper: biorxiv.org/content/early/ Tool: github.com/GATB/DiscoSnp/ Novelties: Clustering per locus Predictions of variants close to sequence extremities Order(s) of magnitude faster than Stack or IPyRAD. Predictions have high precision (up to 99.3% on simulated data) with good recall (82.2% when using high precision parameters) Applied on real biological data, RAD …

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Permanent link to this article: https://team.inria.fr/genscale/discosnp-goes-to-rad-seq/

NEW minimal perfect hash library BBHASH

A preprint for our minimal perfect hash library BBHash (formerly BooPHF) is up on arxiv (http://arxiv.org/abs/1702.03154  ). http://github.com/rizkg/BBHash   

Permanent link to this article: https://team.inria.fr/genscale/new-minimal-perfect-hash-library-bbhash/

New Short Read Connector Release

A new release (1.0.1) of the RConnector tool (connecting reads from large datasets) is available here.

Permanent link to this article: https://team.inria.fr/genscale/new-short-read-connector-release/

GATB Programming Day – Spring 2017

Are you interested in learning how to make high-performance software tools to decypher reads data? Are you a little familiar with C++ programming? Are you happy to come to Spain during Spring 2017? Ok, this event if fully made for you: The Genscale team will hold a GATB Special Session during the 5th International Work-Conference on …

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Permanent link to this article: https://team.inria.fr/genscale/gatb-programming-day-spring-2017/

Slides from the colib’read workshop available

You may find all slides from the colib’read workshop on the program page.

Permanent link to this article: https://team.inria.fr/genscale/slides-from-the-colibread-workshop-available/

Phd subject proposal

We propose a PhD subject about read assembly and haplotyping. See dedicated page

Permanent link to this article: https://team.inria.fr/genscale/phd-subject-proposal/

Workshop Colib’Read – Program Online

Hi all, The Colib’read workshop program is now online on this page http://gdr-bim.cnrs.fr/colibread/program/. We remind you that the attendance is free but ***registration is mandatory*** see website: http://gdr-bim.cnrs.fr/colibread/. Note that space is limited, and registration will be taken in the order received. — WHAT — Calling biological information from raw reads and long reads correction. …

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Permanent link to this article: https://team.inria.fr/genscale/workshop-colibread-program-online/

Short Read Connector presentation

Short Read Connector was published and presented during the Prague Stringology Conference 2016. Slides available from Pierre’s presentation page.

Permanent link to this article: https://team.inria.fr/genscale/short-read-connector-presentation/