{"id":18,"date":"2021-04-14T14:01:08","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/help-sheets\/"},"modified":"2022-02-24T08:25:01","modified_gmt":"2022-02-24T08:25:01","slug":"help-sheets","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/help-sheets\/","title":{"rendered":"Technical help sheet"},"content":{"rendered":"\n

Technical requirements for data analysis<\/h3>\n\n\n\n

You will require the following tools for executing the practicals in this course:<\/p>\n\n\n\n

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

Technical requirements for data analysis You will require the following tools for executing the practicals in this course: 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…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":9,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-18","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/pages\/18","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":6,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":1263,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/pages\/18\/revisions\/1263"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/symbnet-materials\/wp-json\/wp\/v2\/media?parent=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}