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CANGS specifications

Information


Unique identifier OMICS_01084
Name CANGS
Alternative name Cleaning and Analyzing Next Generation Sequences
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
BioPerl, BLAST, MAFFT, MOTHUR, Analytic Rarefaction
Maintained Yes

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Documentation


Maintainer


  • person_outline Christian Schlotterer <>

Publication for Cleaning and Analyzing Next Generation Sequences

CANGS in pipeline

2012
PMCID: 3531709
PMID: 23293637
DOI: 10.3389/fimmu.2012.00386

[…] reads (campbell et al., ). in other studies, all sequences with any type of indel are excluded from analysis (boyd et al., ; wu et al., ) or included without accounting for indels (wu et al., ). cangs (pandey et al., ) identifies indels that appear only in hpts near the primers and discards them. the program does not identify indels occurring far from the primers. varscan (koboldt et al., ) […]


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CANGS in publications

 (5)
PMCID: 5063960
PMID: 27694804
DOI: 10.1038/ncomms12916

[…] candida tropicalis ngs1 to complement the glcnac utilization defect in c. albicans ngs1 mutant. the cross-species experiment showed that ectopically expressed ctngs1 rescued the growth defect in the cangs1 mutant on glcnac (), and partially rescued the defects in the induction of a glcnac catabolic gene (). furthermore, the conserved glcnac binding sites (k175h176) and acetyl-coa interacting […]

PMCID: 3694989
PMID: 23826151
DOI: 10.1371/journal.pone.0066829

[…] searches were based on blastn against the ncbi nucleotide database for fungi excluding uncultured and environmental sequences using the blast based taxonomic assignment script of the software for cleaning and analyzing next generation sequences - cangs ., representative sequences of otus of the fungal its pyrotags assigned under the fungal kingdom were checked for chimeras using the chimera […]

PMCID: 3531709
PMID: 23293637
DOI: 10.3389/fimmu.2012.00386

[…] hts has already been available for several years, there are very few such cleaning programs available for users, and none that can deal with the cleaning of ig genes. for example, the program cangs (pandey et al., ) has a very good pipeline of cleaning sequences, but it discards unique sequences and searches for primers and mid tags with perfect matches only, while it is known that tags […]

PMCID: 3475711
PMID: 23094057
DOI: 10.1371/journal.pone.0047500

[…] to the ncbi taxonomy based on a blast search against the ncbi nucleotide database excluding uncultured sequences and environmental samples followed by a 66% consensus level as implemented in cangs . a total of 1744 reads, which were not assigned to the fungal kingdom were cleared from the sequence dataset., significant correlations with p<0.05 are in bold., significant correlations […]

PMCID: 2916215
PMID: 20609083
DOI: 10.1111/j.1365-294X.2010.04669.x

[…] to be mutation free, otherwise the read was discarded. reads for which an indel was identified at the transition to between read and pcr primer were removed. the detailed clipping algorithm of our cangs package is described elsewhere () and is available from http://i122server.vu-wien.ac.at/pop/software.html., in addition to primer clipping, we removed all sequences that did not fit […]


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CANGS institution(s)
Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Vienna, Austria

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