PMID- 25201145
OWN - NLM
STAT- MEDLINE
DCOM- 20150602
LR  - 20220321
IS  - 1756-0500 (Electronic)
IS  - 1756-0500 (Linking)
VI  - 7
DP  - 2014 Sep 8
TI  - SPANDx: a genomics pipeline for comparative analysis of large haploid whole 
      genome re-sequencing datasets.
PG  - 618
LID - 10.1186/1756-0500-7-618 [doi]
LID - 618
AB  - BACKGROUND: Next-generation sequencing (NGS) is now a commonplace tool for 
      molecular characterisation of virtually any species of interest. Despite the 
      ever-increasing use of NGS in laboratories worldwide, analysis of whole genome 
      re-sequencing (WGS) datasets from start to finish remains nontrivial due to the 
      fragmented nature of NGS software and the lack of experienced bioinformaticists 
      in many research teams. FINDINGS: We describe SPANDx (Synergised Pipeline for 
      Analysis of NGS Data in Linux), a new tool for high-throughput comparative 
      analysis of haploid WGS datasets comprising one through thousands of genomes. 
      SPANDx consolidates several well-validated, open-source packages into a single 
      tool, mitigating the need to learn and manipulate individual NGS programs. SPANDx 
      incorporates BWA for alignment of raw NGS reads against a reference genome or 
      pan-genome, followed by data filtering, variant calling and annotation using 
      Picard, GATK, SAMtools and SnpEff. BEDTools has also been included for genetic 
      locus presence/absence (P/A) determination to easily visualise the core and 
      accessory genomes. Additional SPANDx features include construction of 
      error-corrected single-nucleotide polymorphism (SNP) and insertion-deletion 
      matrices, and P/A matrices, to enable user-friendly visualisation of genetic 
      variants. The SNP matrices generated using VCFtools and GATK are directly 
      importable into PAUP*, PHYLIP or RAxML for downstream phylogenetic analysis. 
      SPANDx has been developed to handle NGS data from Illumina, Ion Personal Genome 
      Machine (PGM) and 454 platforms, and we demonstrate that it has comparable 
      performance across Illumina MiSeq/HiSeq2000 and Ion PGM data. CONCLUSION: SPANDx 
      is an all-in-one tool for comprehensive haploid WGS analysis. SPANDx is open 
      source and is freely available at: http://sourceforge.net/projects/spandx/.
FAU - Sarovich, Derek S
AU  - Sarovich DS
AD  - Global and Tropical Health Division, Menzies School of Health Research, Charles 
      Darwin University, PO Box 41096, Casuarina 0811, NT, Australia. 
      derek.sarovich@menzies.edu.au.
FAU - Price, Erin P
AU  - Price EP
LA  - eng
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140908
PL  - England
TA  - BMC Res Notes
JT  - BMC research notes
JID - 101462768
SB  - IM
MH  - *Genome
MH  - *Haploidy
MH  - Phylogeny
MH  - Polymorphism, Single Nucleotide
PMC - PMC4169827
EDAT- 2014/09/10 06:00
MHDA- 2015/06/03 06:00
PMCR- 2014/09/08
CRDT- 2014/09/10 06:00
PHST- 2014/08/14 00:00 [received]
PHST- 2014/08/27 00:00 [accepted]
PHST- 2014/09/10 06:00 [entrez]
PHST- 2014/09/10 06:00 [pubmed]
PHST- 2015/06/03 06:00 [medline]
PHST- 2014/09/08 00:00 [pmc-release]
AID - 1756-0500-7-618 [pii]
AID - 3161 [pii]
AID - 10.1186/1756-0500-7-618 [doi]
PST - epublish
SO  - BMC Res Notes. 2014 Sep 8;7:618. doi: 10.1186/1756-0500-7-618.