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Introduction：

BBMap (part of the BBTools suite) assesses metagenome assembly quality by mapping original reads back to assembled contigs and computing comprehensive alignment statistics. Unlike simple coverage calculators, it reports read mapping rate, proper pair percentage, indel/substitution rates, and per-contig depth distributions—key indicators of assembly completeness, correctness, and chimerism. It is fast, memory-efficient, and handles large metagenomes on standard hardware.

Workflow Case Analysis Versions Manual Download

Index Assembly: Build BBMap index from contigs.
Map Reads: Align original reads to contigs with error-aware seeding.
Compute Metrics: Aggregate alignment stats (mapping %, identity, insert size, coverage uniformity).
Output: Generate summary statistics file and optional per-contig depth table.

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