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1.  GAGE-B: an evaluation of genome assemblers for bacterial organisms 
Bioinformatics  2013;29(14):1718-1725.
Motivation: A large and rapidly growing number of bacterial organisms have been sequenced by the newest sequencing technologies. Cheaper and faster sequencing technologies make it easy to generate very high coverage of bacterial genomes, but these advances mean that DNA preparation costs can exceed the cost of sequencing for small genomes. The need to contain costs often results in the creation of only a single sequencing library, which in turn introduces new challenges for genome assembly methods.
Results: We evaluated the ability of multiple genome assembly programs to assemble bacterial genomes from a single, deep-coverage library. For our comparison, we chose bacterial species spanning a wide range of GC content and measured the contiguity and accuracy of the resulting assemblies. We compared the assemblies produced by this very high-coverage, one-library strategy to the best assemblies created by two-library sequencing, and we found that remarkably good bacterial assemblies are possible with just one library. We also measured the effect of read length and depth of coverage on assembly quality and determined the values that provide the best results with current algorithms.
Contact: salzberg@jhu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btt273
PMCID: PMC3702249  PMID: 23665771
2.  FLASH: fast length adjustment of short reads to improve genome assemblies 
Bioinformatics  2011;27(21):2957-2963.
Motivation: Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.
Results: We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
Availability and Implementation: The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash.
Contact: t.magoc@gmail.com
doi:10.1093/bioinformatics/btr507
PMCID: PMC3198573  PMID: 21903629
3.  Mugsy: fast multiple alignment of closely related whole genomes 
Bioinformatics  2010;27(3):334-342.
Motivation: The relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution.
Results: We present a new multiple alignment tool for whole genomes named Mugsy. Mugsy is computationally efficient and can align 31 Streptococcus pneumoniae genomes in less than 2 hours producing alignments that compare favorably to other tools. Mugsy is also the fastest program evaluated for the multiple alignment of assembled human chromosome sequences from four individuals. Mugsy does not require a reference sequence, can align mixtures of assembled draft and completed genome data, and is robust in identifying a rich complement of genetic variation including duplications, rearrangements, and large-scale gain and loss of sequence.
Availability: Mugsy is free, open-source software available from http://mugsy.sf.net.
Contact: angiuoli@cs.umd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btq665
PMCID: PMC3031037  PMID: 21148543
4.  It is time to end the patenting of software 
Bioinformatics (Oxford, England)  2006;22(12):1416-1417.
doi:10.1093/bioinformatics/btl167
PMCID: PMC2836512  PMID: 16766564
5.  TopHat: discovering splice junctions with RNA-Seq 
Bioinformatics  2009;25(9):1105-1111.
Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites.
Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development.
Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu
Contact: cole@cs.umd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btp120
PMCID: PMC2672628  PMID: 19289445
6.  Identifying bacterial genes and endosymbiont DNA with Glimmer 
Bioinformatics (Oxford, England)  2007;23(6):673-679.
Motivation:
The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archæa and viruses representing hundreds of species. We describe several major changes to the Glimmer system, including improved methods for identifying both coding regions and start codons. We also describe a new module of Glimmer that can distinguish host and endosymbiont DNA. This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host.
Results:
The new methods dramatically reduce the rate of false-positive predictions, while maintaining Glimmer's 99% sensitivity rate at detecting genes in most species, and they find substantially more correct start sites, as measured by comparisons to known and well-curated genes. We show that our interpolated Markov model (IMM) DNA discriminator correctly separated 99% of the sequences in a recent genome project that produced a mixture of sequences from the bacterium Prochloron didemni and its sea squirt host, Lissoclinum patella.
doi:10.1093/bioinformatics/btm009
PMCID: PMC2387122  PMID: 17237039

Results 1-6 (6)