Article-Journal | Maxime Borry, PhDhttps://maximeborry.com/publication_types/article-journal/Article-JournalHugoBlox Kit (https://hugoblox.com)en-usSat, 01 Aug 2026 00:00:00 +0000https://maximeborry.com/media/icon_hu_61fd8dcb2c2100c3.pngArticle-Journalhttps://maximeborry.com/publication_types/article-journal/De novo assembly and authentication of ancient DNA metagenomes with nf-core/maghttps://maximeborry.com/publication/10-1371-journal-pcbi-1014591/Sat, 01 Aug 2026 00:00:00 +0000https://maximeborry.com/publication/10-1371-journal-pcbi-1014591/nf-core/coproID v2.0: An improved pipeline for the identification of (palaeo)faecal depositorshttps://maximeborry.com/publication/vanos_2026/Sun, 15 Mar 2026 00:00:00 +0000https://maximeborry.com/publication/vanos_2026/Facilitating Accessible, Rapid, and Appropriate Processing of Ancient Metagenomic Data with AMDirThttps://maximeborry.com/publication/borry-facilitating-accessible-rapid-2024/Wed, 01 May 2024 00:00:00 +0000https://maximeborry.com/publication/borry-facilitating-accessible-rapid-2024/TAXPASTA: TAXonomic Profile Aggregation and STAndardisationhttps://maximeborry.com/publication/beber-2023/Tue, 11 Jul 2023 00:00:00 +0000https://maximeborry.com/publication/beber-2023/Natural Products from Reconstructed Bacterial Genomes of the Middle and Upper Paleolithichttps://maximeborry.com/publication/klapper-natural-products-reconstructed-2023/Mon, 01 May 2023 00:00:00 +0000https://maximeborry.com/publication/klapper-natural-products-reconstructed-2023/nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profilinghttps://maximeborry.com/publication/stamouli-2023-10-20-563221/Sun, 01 Jan 2023 00:00:00 +0000https://maximeborry.com/publication/stamouli-2023-10-20-563221/<p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p>sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment fileshttps://maximeborry.com/publication/borry-2022/Wed, 01 Jun 2022 00:00:00 +0000https://maximeborry.com/publication/borry-2022/PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assemblyhttps://maximeborry.com/publication/borry-pydamage-2021/Thu, 01 Jul 2021 00:00:00 +0000https://maximeborry.com/publication/borry-pydamage-2021/Reconstruction of ancient microbial genomes from the human guthttps://maximeborry.com/publication/wibowo-reconstruction-2021/Sat, 01 May 2021 00:00:00 +0000https://maximeborry.com/publication/wibowo-reconstruction-2021/Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eagerhttps://maximeborry.com/publication/yates-reproducible-2021/Mon, 01 Mar 2021 00:00:00 +0000https://maximeborry.com/publication/yates-reproducible-2021/Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDirhttps://maximeborry.com/publication/fellows-yates-community-curated-2021/Fri, 01 Jan 2021 00:00:00 +0000https://maximeborry.com/publication/fellows-yates-community-curated-2021/CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA contenthttps://maximeborry.com/publication/borry-coproid-2020/Wed, 01 Apr 2020 00:00:00 +0000https://maximeborry.com/publication/borry-coproid-2020/Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classificationhttps://maximeborry.com/publication/borry-sourcepredict-2019/Sun, 01 Sep 2019 00:00:00 +0000https://maximeborry.com/publication/borry-sourcepredict-2019/