Fast gapped-read alignment with Bowtie 2

Langmead, Ben, Salzberg, Steven L·2012·Nature Methods
DOI 10.1038/nmeth.1923

Cited by (908)

Items 801–900 of 908

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  95. Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing
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  97. <i>TDP1</i> splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition
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  98. A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation
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  99. Improved Quantification of Circulating Tumor <scp>DNA</scp> in Translocation‐Associated Myxoid Liposarcoma by Simultaneous Detection of Breakpoints and Single Nucleotide Variants
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  100. Type 1 interferon perturbates clonal competition by reshaping human blood development
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