BPGA- an ultra-fast pan-genome analysis pipeline
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
View Archive Info| Field | Value | |
| Title |
BPGA- an ultra-fast pan-genome analysis pipeline
|
|
| Creator |
Chaudhari, Narendrakumar M
Gupta, Vinod Kumar Dutta, Chitra |
|
| Subject |
Structural Biology & Bioinformatics
|
|
| Description |
Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a
paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies
at different scales of phylogenetic resolution. Pan-genome studies provide a framework for estimating
the genomic diversity of the dataset, determining core (conserved), accessory (dispensable) and
unique (strain-specific) gene pool of a species, tracing horizontal gene-flux across strains and providing
insight into species evolution. The existing pan genome software tools suffer from various limitations
like limited datasets, difficult installation/requirements, inadequate functional features etc. Here we
present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven
functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of
novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny,
exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis
and KEGG & COG mapping of core, accessory and unique genes. Other notable features include
minimum running prerequisites, freedom to select the gene clustering method, ultra-fast execution,
user friendly command line interface and high-quality graphics outputs. The performance of BPGA has
been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains.
|
|
| Date |
2016
|
|
| Type |
Article
PeerReviewed |
|
| Format |
application/pdf
|
|
| Identifier |
http://www.eprints.iicb.res.in/2494/1/SCIENTIFIC_REPORTS__Volume__6______Article_Number__24373__.pdf
Chaudhari, Narendrakumar M and Gupta, Vinod Kumar and Dutta, Chitra (2016) BPGA- an ultra-fast pan-genome analysis pipeline. Scientific Reports, 6 (24373). 01p.-10p.. |
|
| Relation |
http://dx.doi.org/10.1038/srep24373
http://www.eprints.iicb.res.in/2494/ |
|