ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates

PLoS Computational Biology
Oliver SchwengersA. Goesmann

Abstract

Whole genome sequencing of bacteria has become daily routine in many fields. Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data. However, comprehensive in-depth analysis of the resulting data remains an arduous and time-consuming task. In order to keep pace with these promising but challenging developments and to transform raw data into valuable information, standardized analyses and scalable software tools are needed. Here, we introduce ASA3P, a fully automatic, locally executable and scalable assembly, annotation and analysis pipeline for bacterial genomes. The pipeline automatically executes necessary data processing steps, i.e. quality clipping and assembly of raw sequencing reads, scaffolding of contigs and annotation of the resulting genome sequences. Furthermore, ASA3P conducts comprehensive genome characterizations and analyses, e.g. taxonomic classification, detection of antibiotic resistance genes and identification of virulence factors. All results are presented via an HTML5 user interface providing aggregated information, interactive visualizations and access to intermediate results in standard bioinformatics file f...Continue Reading

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Citations

Aug 6, 2020·MSystems·Robert A Petit, Timothy D Read
Sep 13, 2020·International Journal of Antimicrobial Agents·Linda FalgenhauerTrinad Chakraborty
Feb 5, 2021·Briefings in Bioinformatics·Yibo DongXiaoming Liu
Jan 9, 2021·Microbiology Resource Announcements·Domonkos SvábIstván Tóth
Dec 29, 2020·Journal of Clinical Microbiology·Trinad ChakrabortyPatrice Nordmann
Apr 30, 2021·Frontiers in Microbiology·Linda FalgenhauerEugen Domann
May 15, 2021·Nucleic Acids Research·Marius Alfred DieckmannAlexander Goesmann

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Datasets Mentioned

BETA
PRJNA215355

Software Mentioned

Trimmomatic
MeDuSa
kmer
VFDB
Minimap2
SnpEff
OpenStack
Fasta
Prokka
MUMmer

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