VAMB

Sample 1 gut microbiome (3 samples from PRJNA795985, 1M read pairs each) co-assembled with Assembly and binned with VAMB v5.0.4, producing 7,212 clusters.

1. 1

   Download 3 samples from PRJNA795985

   for SRR in SRR17531757 SRR17531762 SRR17531772; do fastq-dump --split-files --gzip -X 1000000 --outdir reads/ $SRR; done

   Downloads 1M read pairs per sample (~70 MB compressed each) from the "Diet and Antimicrobial Resistance in Healthy US Adults" study (Shrestha et al., mBio 2022).

2. 2

   Co-assemble all samples with MEGAHIT

   megahit -1 reads/SRR17531757_1.fastq.gz,reads/SRR17531762_1.fastq.gz,reads/SRR17531772_1.fastq.gz -2 reads/SRR17531757_2.fastq.gz,reads/SRR17531762_2.fastq.gz,reads/SRR17531772_2.fastq.gz -o assembly --min-contig-len 1500 -t 8 --presets meta-sensitive

   Produces 14,934 contigs (≥1,500 bp).

3. 3

   Map each sample to contigs

   for SRR in SRR17531757 SRR17531762 SRR17531772; do minimap2 -ax sr -t 8 assembly/final.contigs.fa reads/${SRR}_1.fastq.gz reads/${SRR}_2.fastq.gz | samtools sort -@ 4 -o bams/${SRR}.sorted.bam && samtools index bams/${SRR}.sorted.bam; done

4. 4

   Run VAMB v5.0.4

   vamb bin default --outdir vamb_out --fasta assembly/final.contigs.fa --bamdir bams/ -m 1500 --minfasta 200000 -p 8

   Produces vae_clusters_metadata.tsv with 7,212 clusters (715 normal, 6,472 loner, 25 fallback).