{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:45:58Z","timestamp":1762508758318,"version":"3.37.3"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2022,5,12]],"date-time":"2022-05-12T00:00:00Z","timestamp":1652313600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Next-Generation Sequencing is widely used as a tool for identifying and quantifying microorganisms pooled together in either natural or designed samples. However, a prominent obstacle is achieving correct quantification when the pooled microbes are genetically related. In such cases, the outcome mostly depends on the method used for assigning reads to the individual targets. To address this challenge, we have developed Exodus\u2014a reference-based Python algorithm for quantification of genomes, including those that are highly similar, when they are sequenced together in a single mix. To test Exodus\u2019 performance, we generated both empirical and in silico next-generation sequencing data of mixed genomes. When applying Exodus to these data, we observed median error rates varying between 0% and 0.21% as a function of the complexity of the mix. Importantly, no false negatives were recorded, demonstrating that Exodus\u2019 likelihood of missing an existing genome is very low, even if the genome\u2019s relative abundance is low and similar genomes are present in the same mix. Taken together, these data position Exodus as a reliable tool for identifying and quantifying genomes in mixed samples. Exodus is open source and free to use at: https:\/\/github.com\/ilyavs\/exodus.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Exodus is implemented in Python within a Snakemake framework. It is available on GitHub alongside a docker containing the required dependencies: https:\/\/github.com\/ilyavs\/exodus. The data underlying this article will be shared on reasonable request to the corresponding author.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac319","type":"journal-article","created":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T19:28:25Z","timestamp":1651865305000},"page":"3288-3290","source":"Crossref","is-referenced-by-count":2,"title":["Exodus: sequencing-based pipeline for quantification of pooled variants"],"prefix":"10.1093","volume":"38","author":[{"given":"Ilya","family":"Vainberg-Slutskin","sequence":"first","affiliation":[{"name":"BiomX Ltd. , Ness Ziona 7414002, Israel"}]},{"given":"Noga","family":"Kowalsman","sequence":"additional","affiliation":[{"name":"BiomX Ltd. , Ness Ziona 7414002, Israel"}]},{"given":"Yael","family":"Silberberg","sequence":"additional","affiliation":[{"name":"BiomX Ltd. , Ness Ziona 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