Référentiel des outils installés sur la plateforme Migale

La liste des packages R installés sur la plateforme Migale est disponible ici.

BUSCO (version tous les 2 ans - 2017-11-08)
BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9. BUSCO assessments are implemented in open-source software, with a large selection of lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines. ## DATASET ##  Est-il également possible d'avoir le dataset "Bacteria set" a dispo svp ? Lien vers le dataset : http://busco.ezlab.org/ Merci par avance. Sam
Documentation : http://busco.ezlab.org/
Usage : #busco_env

buster (version 2.10.3 <2016-12-07> - 2016-12-08)
BUSTER structure refinement package. Includes the refine program for running BUSTER refinement and loads of useful utilities.
Remarque : How to cite use of BUSTER :https://www.globalphasing.com/buster/wiki/index.cgi?BusterCite

bwa (version 0.7.12 - 2015-04-07)
BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence, except for disallowing gaps close to the end of the query. It can also be tuned to find a fraction of longer gaps at the cost of speed and of more false alignments.
Usage : #bwa [options]

canu (version 1.6 - 2017-12-26)
Canu is a fork of the Celera Assembler, designed for high-noisesingle-molecule sequencing (such as the PacBio RS II or Oxford NanoporeMinION).
Remarque : Citation: Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. bioRxiv. (2016).
Usage : #canu

cap3 (version 3.0 - 2014-05-06)
Similar to phrap, CAP3 takes individual sequences and assembles them into sequence.s
Usage : #cap3

carthagene (version 1.2 - 2010-10-15)
CarthaGène is a genetic/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. CarthaGène:
Usage : #carthagene

CATCh (version v1 - Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology 75:7537???41.???)
CATCh: an ensemble classifier for chimera detection in 16S rRNA sequencingstudies
Remarque : If you are going to use CATCh, please cite it with the included software (Mothur, WEKA, RDP MultiClassifier 1.1 and DECIPHER):???
Usage : #Mysara M., Saeys Y., Leys N., Raes J., Monsieurs P. 2014. CATCh: an ensemble classifier for chimera detection in 16S rRNA sequencing studies. Under review.???

cd-hit (version 4.6.1 - 2013-08-12)
CD-HIT stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of non-redundant (nr) representative sequences as output.
Remarque : Exemple d utilisation : cd-hit -n 5 -i /db/fasta/nr90/nr90.fsa -o nr80 -M 2048 -c 0.8 -u clstr.lastweek
Usage : #cd-hit [Options]

cd-hit-454 (version - - 2013-08-05)
The 454 pyrosequencing reads contains artificially duplicates, which might lead to misleading conclusions. cdhit-454 is a fast program to identify exact and nearly identical duplicates, the reads begin at the same position but may vary in length or bear mismatches. cdhit-454 can process a dataset in ~10 minutes. it also provides a consensus sequence for each group of duplicates.
Usage : #cd-hit-454

Circlator (version 1.5.3 - 2017-12-26)
Circlator will attempt to identify each circular sequence in an assembly and output a linearised version of it.
Usage : # circlator [options]


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by Dr. Radut