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Introduction：

Coverage calculation using Bowtie2 and SAMtools generates per-contig depth profiles required for metagenome binning with MetaBAT2. Although BBMap can also map reads, the standard MetaBAT2 workflow uses Bowtie2 for alignment and SAMtools for depth extraction, as MetaBAT2’s jgi_summarize_bam_contig_depths script expects BAM files sorted/indexed by coordinate. This coverage matrix (contigs × samples) is essential for differential coverage-based binning.

⚠️ Clarification: Input is raw reads, not BBMap results. If you already have BBMap-aligned BAMs, convert/sort them; otherwise, use Bowtie2 directly.

Workflow Case Analysis Versions Manual Download

Index Assembly: Build Bowtie2 index from assembled contigs.
Align Reads: Map reads to contigs with Bowtie2.
Sort & Index: Convert SAM → sorted BAM + index.
Extract Depth: Run jgi_summarize_bam_contig_depths to generate coverage table(in metabat).

Data

Results

Versions

1. Index contigs

2. Align (paired-end example)

3. Index BAM