| CarveMe | https://github.com/cdanielmachado/carveme |
| SMETANA | https://github.com/cdanielmachado/smetana |
| Snakemake | https://github.com/snakemake/snakemake |
| R | https://www.r-project.org/ |
| Tidyverse | https://github.com/tidyverse/tidyverse |
| ggAlluvial | https://github.com/corybrunson/ggalluvial/ |
| git | https://git-scm.com/ |
| IBM CPLEX Optimizer | https://www.ibm.com/uk-en/products/ilog-cplex-optimization-studio |
| pandas | https://github.com/pandas-dev/pandas |
| seaborn | https://seaborn.pydata.org/ |
| matplotlib | https://matplotlib.org/ |
| framed | https://github.com/cdanielmachado/framed |
| reframed | https://github.com/cdanielmachado/reframed |
| random | https://docs.python.org/3/library/random.html |
| numpy | https://numpy.org/ |
| glob | https://docs.python.org/3/library/glob.html |
| scipy | https://scipy.org/ |
| jupyter | https://jupyter.org/install |
| miniconda | https://docs.conda.io/en/latest/miniconda.html |
| ggpubr | https://cran.r-project.org/web/packages/ggpubr/index.html |
| prodigal | https://github.com/hyattpd/Prodigal |
| python3 | |
| miniconda | https://docs.conda.io/en/latest/miniconda.html |
| text editors (vim, emacs, nano, gedit, vscode) | |
| curl, wget | |
| jq | https://stedolan.github.io/jq/ |
| jupyter | https://jupyter.org/install |
| docker | https://docs.docker.com/get-docker/ |
| sourmash python package | https://sourmash.readthedocs.io/en/latest/ |
| pandas | https://github.com/pandas-dev/pandas |
| metaSPAdes | https://github.com/ablab/spades/releases/tag/v3.15.3 |
| assembly_stats | https://github.com/MikeTrizna/assembly_stats/ |
| Bandage | https://rrwick.github.io/Bandage/ |
| BLAST | https://www.ncbi.nlm.nih.gov/books/NBK569861/ |
| megahit | https://github.com/voutcn/megahit |
| bwa | https://sourceforge.net/projects/bio-bwa/files/ |
| samtools | https://sourceforge.net/projects/samtools/files/samtools/ |
| MetaBAT | https://bitbucket.org/berkeleylab/metabat/downloads/ |
| CheckM | https://github.com/Ecogenomics/CheckM |
| newick utils | https://github.com/tjunier/newick_utils |
| FigTree | https://github.com/rambaut/figtree |
| Java Runtime Environment | |
| fastqc | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| multiqc | https://github.com/ewels/MultiQC |
| bowtie2 | https://github.com/BenLangmead/bowtie2 |
| biobakey-kneaddata | https://github.com/biobakery/kneaddata |
| blast extecutables (blastn, makeblastdb) | https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download |
| kraken2 | https://github.com/DerrickWood/kraken2 |
