bio-assembly-qc

Automate genome assembly and QC by running SPAdes for short reads or Flye for long reads, then executing QUAST or MetaQUAST to generate contig metrics and QC reports in the results directory.

Yes, this assembly QC workflow supports hybrid long-read and short-read datasets by selecting the appropriate assembler, such as Flye or SPAdes, based on the input read type and genome size.

To run metagenome assembly and generate QUAST reports, you need a Pixi or conda-enabled environment, input reads in fastq.gz format, and a supported assembler like SPAdes or Flye.

Use MetaQUAST instead of QUAST for metagenome assembly evaluation when assessing bacterial, archaeal, or viral metagenome assemblies to produce specialized reference-based contig metrics and QC reports.

Yes, you can assemble bacterial, archaeal, and viral isolate genomes with this automated pipeline, which handles isolate assemblies alongside metagenomes using resource-aware settings and quality gates.

Metagenome assembly quality gates may fail due to insufficient input read quality in fastq.gz files, inappropriate assembler selection for your read type, or inadequate resource allocation in the Pixi or conda environment.