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Trends in amino acid usage across the class Mollicutes.
Iriarte A, Baraibar JD, Diana L, Castro-Sowinski S, Romero H, Musto H.
Source
a Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias , UDELAR. Iguá 4225 , Montevideo , 11400 , Uruguay.-------------------------------------------------
Abstract
Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new challenges, including a need for efficient algorithms for the assembly of genomes from short reads and forresolving repetitions. Additionally after abinitioassembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data generatedby assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs ofEscherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed redundantsequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome assembly in tests with data from Prokaryotic organisms.
Availability
Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher.
Keywords: NGS sequencing, ab initio assembly of genomes, redundant sequences
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Background
NGS platforms utilize various different strategies for sequencing genomes and are capable of generating a large quantity of data with great accuracy and reduction in time necessary for sequencing and cost per base [1, 2]. However, they require considerable computational infrastructure for data processing [3]. The reduced size of the sequences that areinitially generated presents challenges for the genome assembly process, including resolution of repetitive regions and a need to process extremely large numbers of reads, several magnitudes greater than produced by previous technologies [4].
Among strategies for obtaining complete genomes via NGS, there are hybrid approaches, involving the use of various assembly algorithms and combinations ofdata from various sequencing platforms to take advantage of complementarity among data sets. The redundancy of reads gives greater coverage of sequencing, which favors the generation of contigs that can represent regions in common or new regions of the genome, depending on the methodologies that are chosen [5]. The large number of contigs generated by these approaches demand considerablecomputational and human resources for their analysis, mainly for the identification of assembly errors and for elimination of the few wrong bases at the ends of contigs, which prevents overlapping extension due to mismatches [6–8].
To this end, we developed Simplifier; a stand-alone application that eliminates redundant sequences from groups of contigs generated by ab initio methodology, facilitatinganalysis of the data, reducing the time needed for the finalization and curation of the genome assemblies.
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Software
Input and output
Data:
The data that we tested with this software were obtained by sequencing Escherichia coli DH10Bhttp://www.ncbi.nlm.nih.gov/sra/SRX000353 with the SOLiD Version 3 sequencer; it provided a 50x50 mate-paired...