De novo Assembly
Sam Minot edited this page Feb 7, 2020
·
2 revisions
To identify microbial genes, geneshot will:
- perform de novo assembly of short reads with MEGAHIT,
- identify protein-coding sequences with Prodigal, and
- deduplicate similar gene sequences using MMseqs2
Various flags include:
-
--phred_offset: The PHRED offset used by MEGAHIT, default: 33 -
--min_identity: Amino acid identity cutoff used by MMseqs2 to combine similar genes, default: 90 -
--min_coverage: Length cutoff used by MMseqs2 to combine similar genes, default: 50
- Getting Started
- De novo vs. Reference-Based Analysis
- Running Geneshot
- Output Files
- Input File Format
- Nextflow Configuration
- Helpful Scripts:
- Concepts: