abyssMG

Bioinformatics analysis and reproducible workflows for the study of ammonia-oxidizing archaea in abyssal and hadal surface sediments

In this repository you will find the scripts necessary to replicate the results shown in the following paper: Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

• The raw data can be accessed here on ENA

• The reconstructed MAGs discussed in the paper can be found here on ENA, and complete Anvi’o databases for these MAGs can be found here

• The following scripts can be used to reproduce the results presented in the paper:
  • M1: All steps for MAG reconstruction using Anvi’o’s snakemake workflows
  • M2: Download and introduction of external MAGs in Anvi’o as references
  • M3: Identification of amoA genes in the MAGs and external genomes and placement in the tree by Alves et al., 2018. Computation of de novo phylogenomic tree using GTDB-tk and IQ-tree.
  • M4: Production of the figures and statistical analyses. NB: figures were refined for publication using Affinity Designer (placement of legends, color coding…)
• This archive contains all the snakemake config and text files used for the analysis presented in this paper