Recommended Reading - AstrobioMike/JPL-HBCU-2020 GitHub Wiki

Tools

Kraken: ultrafast metagenomic sequence classification using exact alignments, Wood and Salzberg 2014
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Improved metagenomic analysis with Kraken 2, Wood et al. 2019
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Bracken: estimating species abundance in metagenomics data, Lu et al. 2017
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Ganon, Piro et al. 2020 PDF download

Centrifuge, Kim et al. 2016
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Benchmarking papers

Benchmarking metagenomics tools for taxonomic classification, Ye et al. 2019
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Shotgun metagenomics, from sampling to analysis, Quince, et al. 2017
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Critical assessment of metagenome interpretation – a benchmark of metagenomics software, Sczyrba et al, 2017
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Comprehensive benchmarking and ensemble approaches for metagenomic classifiers, McIntyre et al. 2017
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An evaluation of the accuracy and speed of metagenome analysis tools, Lindgreen et al. 2016
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Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities, Peabody et al. 2015
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General

Bioinformatics – An introduction for computer scientists, Cohen 2004
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