Référentiel des outils installés sur la plateforme Migale

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

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]

circos (version 0.64 - 2013-01-20)
Circos is a software package for visualizing data and information. Itvisualizes data in a circular layout — this makes Circos ideal for exploringrelationships between objects or positions. There are other reasons why acircular layout is advantageous, not the least being the fact that it isattractive.
Usage : #circos

clustal-omega (version 1.1.0 - 2012-07-17)
Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks.
Remarque : Citing Clustal:Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7.
Usage : #clustalo --help

clustalx (version 2.1 - 2013-12-29)
Multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.
Usage : #clustalx (en mode graphique) ou clustalw2 (en mode ligne de commande)


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by Dr. Radut