dependencies_description.md

Dependencies

Metawrap

• Metawrap uses python version of 2.7.14.

Tool link: https://github.com/bxlab/metaWRAP

Dependencies
Database Checkm_DB
Database KRAKEN standard database
Database KRAKEN2 standard database
Database NCBI_nt
Database NCBI_tax
Database Indexed hg38
GCC/6.4.0-2.28
OpenMPI/2.1.2

The Databases can be installed by following the instructons of the following hyperlink: Databases_metaWrap.

GTDB-Tk

Tool link: https://academic.oup.com/bioinformatics/article/36/6/1925/5626182

• GTDB-Tk uses Python version >=3.6 (3.6.4).

Dependencies	Version
Library OpenMPI	2.1.2
Package GCC	6.4.0-2.28
Lirbrary DendroPy	>= 4.1.0
Lirbrary NumPy	>= 1.9.0
Lirbrary tqdm	>= 4.31.0
Software Prodigal	>= 2.6.2
Software HMMER	>= 3.1b2
Software pplacer	>= 1.1
Software FastANI	>= 1.32
Software FastTree	>= 2.1.9
Software Mash	>= 2.2

• The dependencies of GTDB-Tk can be found in the following webpage: https://ecogenomics.github.io/GTDBTk/installing/index.html.

CheckM

Tool link: https://genome.cshlp.org/content/25/7/1043

• CheckM uses Python version 3.7.4.

Dependencies	Version
Package GCCcore	8.3.0
Software HMMER	>=3.1b1
Software Prodigal	2.60 or >=2.6.1
Software pplacer	>=1.1
Lirbrary NumPy	>= 1.9.0
Lirbrary tqdm	>= 4.31.0
Software Prodigal	>= 2.6.2

• As pplacer requires also dependencies, these dependencies, together with instructions of how to install them, can be found in the following link: http://matsen.github.io/pplacer/compiling.html.

PROKKA

Tool link: https://academic.oup.com/bioinformatics/article/30/14/2068/2390517

BBTools

Tool link: https://sourceforge.net/projects/bbmap/

VirSorter2

Tool link: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00990-y

Dependencies
Software HMMER of version 3.1b2
Software MCL
Software Metagene Annotator
Software MUSCLE
Software BLAST+
Software DIAMOND
Package gcc/4/8.1-3

• The software used in the VirSorter can be found also in the following hyperlink: Software_VirSorter.

CheckV

Tool link: https://www.nature.com/articles/s41587-020-00774-7

• For CheckV to work the installation of Anaconda3/5.3.0 with python version of 3.6 is required.

Dependencies	Version
Software DIAMOND	2.0.4
Software HMMER	3.3
Software Prodigal	2.6.3

• More information about CheckV dependencies can be found by following the webpage: https://bitbucket.org/berkeleylab/checkv/src/master/.

vContact2

Tool link: https://www.nature.com/articles/s41587-019-0100-8

• vContact2 uses Anaconda3/5.3.0 and python of version >=3.7 (3.7.4 ).

Dependencies	Version
Package GCCcore	8.3.0
Package Java/11.0.2
biopython	>=1.73
hdf5	>=1.10.4
networkx	>=2.2
numpy	>=1.15.4
pandas	>=0.25.0,<=0.25.3
psutil	>=5.5.0
pyparsing	>=2.4.6
pytables	>=3.4.0
scikit-learn	>=0.20.2
scipy	>=1.2.0

• More information about vContact2 dependencies can be found by following the webpage: https://bioconda.github.io/recipes/vcontact2/README.html.

VIBRANT

Tool link: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00867-0

• VIBRANT uses python of version >= 3.5 (3.6.6).

Dependencies
KEGG
Pfam (v32)
VOG (release 94)
Package GCC/7.3.0-2.30
Package OpenMPI/3.1.1
Prodigal version 2.6.3
HMMER3
gzip
tar
wget
BioPython
Pandas
Matplotlib
Seaborn
Numpy (version >= 1.17.0)
Scikit-learn (version == 0.21.3)
Pickle

• More information about VIBRANT dependencies can be found in the following hyperlink: VIBRANT_Dependencies.

Stampede-clustergenomes

Tool link: https://bitbucket.org/MAVERICLab/stampede-clustergenomes/src/master/

• Stampede-clustergenomes uses python of version 2.7.14.

Packages	Version
MUMmer	3.0
GCCcore	6.4.0
libtool	2.4.6
Perl	5.26.0
OpenMPI	2.1.2
GLib	2.54.3

• Instructions for installation of Perl/5.26.0 and MUMmer/3.0 can be found in the following webpage: https://bitbucket.org/MAVERICLab/stampede-clustergenomes/src/master/.

VirFinder

Tool link: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0283-5

• VirFinder uses R/3.4.4. Also the user need to have OpenMPI/2.1.2 library installed.

Dependencies
R package glmnet
R package Rcpp
R package qvalue
Package GCC/6.4.0-2.28
Package OpenMPI/2.1.2

WIsH

Tool link: https://academic.oup.com/bioinformatics/article/33/19/3113/3964377

• WIsH requires OpenMP library installed.

EukRep

Tool link: https://genome.cshlp.org/content/28/4/569

• EukRep uses python of version 3.6.4.

Dependencies
GCC/6.4.0-2.28

MAKER2

Tool link: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-491

Dependencies
RepeatModeler(1.0.4)
RepeatMasker (4.0.5)
GCC/6.4.0-2.28
RepBase (version used was 20150807)
MAKER/2.31.10-foss-2019b-1
Augustus version 3.3
BUSCO version 3
SNAP
BEDtools version 2.24.0

• As SNAP requires some more dependencies, they can be found in the following hyperlink: Compiling_snap.
• As RepeatModeler(1.0.4) requires some more dependencies,they can be found in the following hyperlink: RepeatModeler_dependencies.
• As RepeatMasker (4.0.5) requires some more dependencies, they can be found in the following link: http://www.repeatmasker.org/RepeatMasker/.
• As Augustus requires some more dependencies, they can be found in the following hyperlink: Dependencies_Augustus.
• As BEDtools requires some more dependencies, they can be found in the following link: https://bedtools.readthedocs.io/en/latest/content/installation.html.
• About Busco, the user can check the following hyperlink: BUSCO_Manual.
• More information about MAKER2 dependencies can be found in the following hyperlink: Maker2_Software prerequisites.

BUSCO

Tool link: https://academic.oup.com/bioinformatics/article/31/19/3210/211866

• BUSCO uses python of version 3.7.4.

Dependencies
Package GCC/6.4.0-2.28
Package OpenMPI/2.1.2
foss/2019b
NCBI BLAST+
HMMER 3.1b2
Augustus 3.0.x

• As Augustus requires some more dependencies, they can be found in the following hyperlink: Dependencies_Augustus.
• More information about BUSCO dependencies can be found in the following hyperlink:BUSCO_Dependencies.

EukCC

Tool link: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02155-4

• The EukCC uses python of version 3.7.4.

Dependencies for EukCC
Package GCCcore/8.3.0
Package foss/2019b
Perl/5.30.0
Anaconda2/5.3.0
Package foss-2019b

• More information about EukCC dependencies can be found by following the webpage: https://eukcc.readthedocs.io/en/latest/install.html#install-via-conda.

GeneMark-ES

Tool link: https://academic.oup.com/nar/article/29/12/2607/1034721 ...

Ani_Splitter

Dependencies
Package GCCcore/8.3.0
Package OpenMPI/3.1.4
R
cluster
dendextend
dplyr
fpc
ggplot2
reshape2
rlang
tidyselect
vctrs

Bowtie

Dependencies
Python 3.6.6
OpenMPI 3.1.1
GCC 7.3.0-2.30
datamash-1.3
Bowtie2 2.3.5.1
SAM tools 1.9

• More information about Bowtie 2 can be found by following the webpage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml.
• More information about Samtools can be found by following the webpage: http://www.htslib.org/doc/samtools.html.