Article-Journal

De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag

Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both …

nf-core/coproID v2.0: An improved pipeline for the identification of (palaeo)faecal depositors

Facilitating Accessible, Rapid, and Appropriate Processing of Ancient Metagenomic Data with AMDirT

Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances …

TAXPASTA: TAXonomic Profile Aggregation and STAndardisation

TAXPASTA is a standalone command-line tool written in Python that aims to standardise the diverse range of metagenomic profiler output formats to simple tabular formats that are …

Natural Products from Reconstructed Bacterial Genomes of the Middle and Upper Paleolithic

Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this …

nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling

Metagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and …

sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files

sam2lca is a program performing reference sequence disambiguation for reads mapping to multiple reference sequences in a shotgun metagenomics sequencing dataset. To do so, it takes …

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to …

Reconstruction of ancient microbial genomes from the human gut

Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, …

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and …

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen …

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. …

Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification

SourcePredict is a Python package distributed through Conda, to classify and predict the origin of metagenomic samples, given a reference dataset of known origins, a problem also …