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CRAC specifications

Information


Unique identifier OMICS_01240
Name CRAC
Alternative name Complex Reads Analysis & Classification
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_01240
Name CRAC
Alternative name Complex Reads Analysis & Classification
Interface Web user interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Programming languages C++
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline CRAC <>

Additional information


A free trial is available on the site.

Publication for Complex Reads Analysis & Classification

CRAC in publications

 (5)
PMCID: 5861515
PMID: 29623188
DOI: 10.5256/f1000research.12254.r25101

[…] to efficiently identify novel genes/exons, splice isoforms, rna editing, allele-specific mutations, differential gene expression and fusion-transcripts or chimeric rna (chrna)., methods: we used crac, a tool that uses genomic locations and local coverage to classify biological events and directly infer splice and chimeric junctions within a single read. crac’s algorithm extracts […]

PMCID: 5090896
PMID: 27822312
DOI: 10.1186/s13040-016-0112-6

[…] pipeline (fig. ) using the above genome simulation procedure along with i) the generation of corresponding rna-seq reads by flux simulator [] and ii) labelling chrnas classes through the use of crac software []. fig. 1 , crac has been chosen to perform this experimental study for two main reasons. first of all, it is a splice-aware mapping software that integrates the identification […]

PMCID: 4828881
PMID: 27067391
DOI: 10.1186/s12920-016-0178-5

[…] (fig. ). sequencing data were demultiplexed and aligned to the specific chromosomes of our sequenced genes (hg19) using both casava (consensus assessment of sequencing and variation; v1.8.2) [] and crac (complex reads analysis and classification; v1.3.0) [] software. alignments were prepared for variant calling using picard [] and variant calling was performed on both versions of the aligned […]

PMCID: 4378021
PMID: 25494611
DOI: 10.1186/1471-2164-15-1103

[…] the assembly was obtained from the show-coords files (-l -c -b -t -o –r)., gap closing was performed in 4 steps using the ot-2009 dataset (1) de novo assembly, (2) image and (3) pcr sequencing (4) crac. de novo scaffolds recruitment to close gaps in the reference genome sequence was done as follows. de novo scaffolds were aligned onto the reference genome sequence using blastn. if the scaffold […]

PMCID: 3868316
PMID: 24252160
DOI: 10.1186/1748-7188-8-25

[…] in the reference genome), so spliced mappings must be looked for, which is unusual for standard dna reads mapping. some mappers for this problem also make use of the fm-index, e.g., tophat [] and crac []. a comprehensive list of rna-seq mapping approaches can be found in []., the fm-index searches for a pattern finding its successive letters, from right to left, which can be called backward […]


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CRAC institution(s)
Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), UMR 5506, CNRS and Université de Montpellier 2, Montpellier, France

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