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FLASH: fast length adjustment of short reads to improve genome assemblies
FLASH is a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short and when FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. Expand
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Evaluating several of the leading de novo assembly algorithms on four different short-read data sets generated by Illumina sequencers concludes that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome. Expand
Genomic signatures of evolutionary transitions from solitary to group living
There is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings and these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Expand
GAGE-B: an evaluation of genome assemblers for bacterial organisms
This work compared the assemblies produced by this very high-coverage, one-library strategy to the best assemblies created by two-library sequencing, and found that remarkably good bacterial assemblies are possible with just one library. Expand
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes
EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) processes the raw data from an RNA-seq experiment on a bacterial or archaeal species and produces estimates of the expression levels for each gene in these gene-dense genomes. Expand
Genomic Features of a Bumble Bee Symbiont Reflect Its Host Environment
The genome of one gammaproteobacterial member of the gut microbiota, for which the name “Candidatus Schmidhempelia bombi” is proposed, is reported that was inadvertently sequenced alongside the genome of its host, the bumble bee, Bombus impatiens. Expand