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

Abstract

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 scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.

Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

“…Raw sequencing reads were processed with nf-core/eager ( 90 ) (v2.2.2), with the exception of I5884 and I2470 samples that required a preprocessing step to remove the 7-bp internal barcodes ( SI Appendix ). In short, adapters were trimmed with AdapterRemoval v2.3.1 ( 91 ).…”

Ancient dental calculus preserves signatures of biofilm succession and inter-individual variation independent of dental pathology

“…These published historic dental calculus samples were downloaded from ENA and processed with the nf-core/eager pipeline (Fellows Yates et al, 2021a), described above. For analyses of pre- and post-tobacco introduction populations, post-medieval individuals from RAD, MID, and CMB were treated as smokers and medieval individuals from KIL, ELR, and IVE were treated as non-smokers, since no tobacco products were available in Europe during the lifetime of these individuals.…”

“…All raw data were processed using the nf-core/eager pipeline (Fellows Yates et al, 2021a), version 2.1.0. This included quality checks with FastQC (Andrews, 2010), adapter trimming, read collapsing, and quality filtering with AdapterRemoval (Schubert et al, 2016), and mapping against the human genome (HG19) with bwa aln -n 0.02 -l 1024 (Li and Durbin, 2009) and samtools (Danecek et al, 2021) to remove human reads.…”

A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species

“…Libraries were amplified by indexing PCR which introduced 8 bp tags on both ends, pooled and sequenced using a 75 paired-end (PE) approach on a lane of an Illumina HiSeq 2500 system (pool containing 20 sample libraries with a lower fraction for four extraction blank libraries). Libraries were then processed using the ancient DNA pipeline EAGER ( Fellows Yates et al 2021 ) as well as tools already integrated in samtools ( Li et al 2009 ).…”

“…After sequencing, reads were split into cram files for each library based on matching 8 bp tags, converted into FASTQ files and processed using the ancient DNA analysis pipeline EAGER ( Fellows Yates et al 2021 ) (nextflow version 20.10.0, EAGER last modified December 2020). The following parameters were used: adapter sequence trimming (forward AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, reverse AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTNNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT), aligning to the An.…”