Bioinformatics · 2017 · 2K citations · 16 references
Life SciencesBioinformaticsGeneticsGenome EvolutionGenomic Data AnalysisGenomicsComputational GenomicsDna SequencingGenome SequencingNext-generation SequencingPhylogenomic AnalysisVariant AnalysisComparative Genome EvolutionGenome Size EstimationHeterozygosity EstimationReference-free Variant AnalysisShort-read Sequencing
SUMMARY: GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates. AVAILABILITY AND IMPLEMENTATION: http://genomescope.org , https://github.com/schatzlab/genomescope.git . CONTACT: mschatz@jhu.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
Heng Li · arXiv (Cornell University) · 2014 · 5.8K citations · Full text