Omar Ahmed

Omar Ahmed

PhD Student at Johns Hopkins University

Publications

A list of my publications can also be found at my Google Scholar profile.

Pan-genomic Matching Statistics for Targeted Nanopore Sequencing

Published in iScience, 2021

This paper introduced a tool called SPUMONI which performs rapid, binary classification of reads with respect to a reference database. The tool is aimed toward the application of adaptive sequencing with Nanopore sequencers.

Recommended citation: Ahmed, O., Rossi, M., Kovaka, S., Schatz, M. C., Gagie, T., Boucher, C., & Langmead, B. (2021). Pan-genomic Matching Statistics for Targeted Nanopore Sequencing. iScience, 102696.

Megadepth: efficient coverage quantification for BigWigs and BAMs

Published in Bioinformatics, 2021

This paper presented a new efficient tool for quantifying coverage for BigWigs and BAMS called megadepth. This tool was developed by Christopher Wilks. I assisted in the benchmarking of the tool for the paper.

Recommended citation: Wilks, C., Ahmed, O., Baker, D. N., Zhang, D., Collado-Torres, L., & Langmead, B. (2021). Megadepth: efficient coverage quantification for BigWigs and BAMs. Bioinformatics (Oxford, England), btab152. https://doi.org/10.1093/bioinformatics/btab152