sbx_assembly

A Sunbeam extension for assembly of contigs using Megahit, gene annotation using Prodigal, and annotation using Blast and Diamond. It can also map reads to contigs and calculat per-base coverage using Minimap2 and samtools.

Configuration

sbx_assembly

• min_length: Is the minimum contig length to accept in the final filtering abx_annotation
• threads: Is the number of threads to use running blast/diamond
• circular_kmin: Is the minimum length of overlap to check for circular contigs with
• circular_kmax: Is the maximum length of overlap to check for circular contigs with
• circular_min_len: Is the minimum sequence length to consider checking for circularity sbx_coverage
• threads: Is the number of threads to use while running minimap2 and samtools sort

Docs

More docs.