Nanopore base calling and hybrid metagenomic assembly

Base calling was performed on a Lambda Labs workstation containing two NVIDIA RTX 3090 graphical processing units (GPUs) with Guppy v6.1.2 using the following settings: –chunk_size 3000 –chunks_per_runner 768 –qscore_filtering –min_qscore 7 –config dna_r9.4.1_450bps_hac.cfg –calib_detect –compress_fastq.

To assemble MAGs from Illumina and Nanopore data from chimpanzees, we employed the reticulatus snakemake workflow (https://github.com/SamStudio8/reticulatus). All GPU-accelerated assembly and polishing was conducted on a Lambda Labs workstation containing two NVIDIA RTX 3090 GPUs. Pan reads were removed from fastq files using dehumanizer against Pan reference genome GCF_002880755.1. Nanopore reads for each sample were assembled into contigs with Flye v2.9⁵⁶ and contigs were polished with racon v1.4.3⁵⁷ and medaka v1.4.0 (https://github.com/nanoporetech/medaka) using Illumina reads derived from each faecal sample sequenced on a MinION.