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BBMap: A Fast, Accurate, Splice-Aware Aligner
Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding,Expand
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BBMerge – Accurate paired shotgun read merging via overlap
Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping,Expand
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Omega: an Overlap-graph de novo Assembler for Metagenomics
MOTIVATION Metagenomic sequencing allows reconstruction of microbial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed for assembling andExpand
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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread throughExpand
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Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California
Epidemic in Northern California Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks is valuable for tracing the sources and perhaps for drawing lessons aboutExpand
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High-resolution phylogenetic microbial community profiling
Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to newExpand
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Murine colitis reveals a disease-associated bacteriophage community
The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseasesExpand
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Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics:
Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionaryExpand
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Chapter One – Fungal Genomics: Sequencing and Annotation
Abstract Plants grow in close associations with fungi—pathogens, symbionts, and endophytes—and depend on these associations for success. Therefore, understanding the mechanisms of these interactionsExpand
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Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection.
In previous work (D. R. Harris et al., J Bacteriol 191:5240-5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne et al., Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), weExpand
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