Référentiel des outils installés sur la plateforme Migale

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

bowtie2 (version 2.2.5 - 2015-04-07)
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Usage : #bowtie2 [options]* -x {-1 -2 | -U } [-S ]

breakdancer (version 1.4.5 - 2015-03-06)
BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.
Usage : #Usage: breakdancer-max

bsmap (version 2.90 - 2015-03-17)
BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.
Remarque : Citation: Xi Y, Li W: BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics (2009) 10:232.
Usage : #bsmap

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.???


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