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Genome Assembly

This module includes:De novo assembly
Reads quality analysis
(more info)

Use custom options only if the result of default assembly is poor

Custom assembly options

Genome assembly is disabled. In order to run other modules, you must provide a set of assembled contigs.

Comparative Genomics

This module includes:Genome alignment to a reference sequence
Linear and circular alignment plotting
Detection of gaps and missing regions
Contig reordering based on reference genome
Variant calling and SNP annotation from reads
(more info)

Bacterial Classification and Annotation

This module includes:Taxonomic classification
Multilocus sequence typing
Genome annotation
Identification of plasmids
Identification of virulence factors
(more info)

Two best-scoring sequence hits per alignment, at least 500 bp, 90% identity

Two best-scoring sequence hits per alignment, at least 90% identity