Assembly & Annotation

Note

This is not a guide for getting started with Metasmith. See the tutorial instead.

Usage

Metasmith includes a built-in library of transformations covering common workflows in genomic assembly and functional annotation.

from metasmith.python_api import *
dtypes, containers, transforms = Std()

• dtypes: the data types provided by the library

• transforms: the transforms provided by the library

• containers: a data instance library providing containers for execution of the transforms

You can use these APIs when generating a workflow. For example:

smith.GenerateWorkflow(
    samples    = [inputs],
    resources  = [containers],
    transforms = [transforms],
    targets    = [dtypes["functional_annotation"]]
)

assuming inputs is a DataInstanceLibrary with some user-provided inputs.

Data Types

The assembly and annotation library provides the following data types:

Quality Control

• read_stats: short OR long read quality stats

Assembly

• long_reads_filtered: filtered to remove low-quality reads (based on length and identity)

• long_reads_assembly

• short_reads_trimmed: quality trimmed and adapters clipped

• short_reads_assembly

• sequence_alignment_map: short reads mapped on a draft assembly built with long reads

• binary_alignment_map: binary version of sequence_alignment_map

• hybrid_assembly: long read draft assembly improved with short reads

• assembly: a generic type over short_reads_assembly, long_reads_assembly, or hybrid_assembly

Annotation

Databases

• bakta_database: the BAKTA database, hosted here

  • bakta_database_light: the lightweight BAKTA database

  • bakta_database_full: the default BAKTA database

• Kofamscan

  • kofamscan_profile: the Kofamscan profile database, hosted here

  • kofamscan_ko_list: the Kofamscan KO identifier database, hosted here

• cazy_ref: the CAZy database, hosted here

• BUSCO

  • All lineage databases are hosted here

  • busco_ref: the refseq_db.faa file from a lineage database

  • busco_map: the species.info file from a lineage database

Annotation outputs

• coding_sequences: a FASTA of all predicted coding sequences

• gene_features: a GFF3 annotation file including genomic coordinates and other metadata

• bakta_annotations: a genome annotated by BAKTA

• kofamscan_annotations: a genome annotated by Kofamscan

• cazy_annotations: a BLAST-style TSV of CDS hits against CAZy

• busco_annotations: a BLAST-style TSV of CDS hits against BUSCO

• functional_annotations: a compiled directory of all annotation outputs