Référentiel des outils installés sur la plateforme Migale

canu (version 1.3 - 2016-10-18)
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

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)

cluster-3.0 (version 3.0 - 2013-05-24)
The open source clustering software available here implement the most commonly used clustering methods for gene expression data analysis. The clustering methods can be used in several ways.Cluster 3.0 provides a Graphical UserInterface to access to the clustering routines. It is available for Windows, Mac OS X, and Linux/Unix. Python users can access the clustering routines by using Pycluster, which is an extension module to Python. People that want to make use of the clustering algorithms in their own C, C++, or Fortran programs can download the source code of the C Clustering Library.
Usage : #cluster


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by Dr. Radut