Written 2023, by Rachael Storo. Contributions by Giles Goetz. Based on a workflow written by Nastassia Patin. v. 1.0
- Amethyst requires python >3.6
- Amethyst requires data files to be located in amethyst/00_data/fastq, separated in R1 for forward reads, R2 for reverse.
- Raw data files must be UNZIPPED to be processed.
To get started, please see the Quick Start Guide
Note- this is a prioritized list of features to add to Amethyst. This is subject to change.
| Program | Function | Status |
|---|---|---|
| fastqc | read QC | complete |
| multiqc | read QC | complete |
| multitrim | read trimming | complete |
| megahit | assembly | complete |
| bbnorm | normalization | ON HOLD |
| bowtie2 | assembly coverage analysis | complete |
| prodigal | gene prediction | complete |
| prokka | gene annotation | complete |
| sourmash | diversity analysis- assembly based | complete |
| maxbin2 | binning | complete |
| checkm | bin/MAG quality | complete |
| dRep | dereplication of bins/MAGs | complete |
| GTDB-Tk | taxonomic assignment of bins/MAGs | complete |
| nonpareil | read-based coverage analysis | backlog |
| sourmash | diversity analysis- read based | backlog |
| humann | functional analysis | backlog |
*BBnorm is on hold as normalization is not ideal for binning, and it was having errors.
Features to add in new versions:
- co-assembly capabilities
- overarching rules to combine pseudo rules
- benchmarking/logs- coded in the current version but not writing
- init file to make all conda environments needed to run amethyst
- yaml files for conda environments needed to run amethyst
- choice of assembler
- Docker Containers