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Title:	Microbiome Analysis Infrastructure Roadmap V1.1
Owner:	Roberto Barrero Gumiel
Creator:	Roberto Barrero Gumiel	Dec 07, 2020
Last Changed by:	Roberto Barrero Gumiel	Dec 07, 2020
Tiny Link: (useful for email)	https://eresearchqut.atlassian.net/wiki/x/CoBvMg
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Time	Editor
Dec 07, 2020 00:34	Roberto Barrero Gumiel	View Changes
Dec 07, 2020 00:33	Roberto Barrero Gumiel	View Changes
Dec 07, 2020 00:28	Roberto Barrero Gumiel

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Outgoing Links

External Links (176)

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-gu…

metaphyler.cbcb.umd.edu/

bcb.unl.edu/dbCAN2/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965101/

https://github.com/edgraham/BinSanity

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1334385/

https://www.ebi.ac.uk/services/tara-oceans-data

www.gromacs.org/

https://github.com/lh3/minimap2

https://pyani.readthedocs.io/_/downloads/en/latest/pdf/

https://news.aarnet.edu.au/cloudstor-integration-for-galaxy…

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411777/

microbiomeutil.sourceforge.net/

https://github.com/rhetorica/gist

https://cab.spbu.ru/software/spades/

https://greengenes.secondgenome.com/

www.usadellab.org/cms/?page=trimmomatic

https://rstudio.com/

www.taraoceans-dataportal.org/top/;jsessionid=0721763036216…

https://github.com/fenderglass/Flye

https://www.mothur.org/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965039/

hmmer.org/

https://www.bioconductor.org/packages/release/bioc/html/phy…

https://request.usegalaxy.org.au/

https://github.com/Ecogenomics/GTDBTk

https://github.com/biocore/sortmerna

https://www.biorxiv.org/content/10.1101/074252v1.full

https://pubmed.ncbi.nlm.nih.gov/22821567/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051327/

https://github.com/marbl/VALET

https://github.com/mbanf/METACLUSTER

https://jupyter.org/

https://docs.google.com/spreadsheets/d/1SwmheBcmHkvvzfcvRUk…

www.funguild.org/

www.cazy.org/

www.bioinformatics.babraham.ac.uk/projects/fastqc/

https://geronimp.github.io/graftM/

https://www.nextflow.io/

https://vamps2.mbl.edu/

merenlab.org/software/anvio/

mailto:communities@biocommons.org.au

https://academic.oup.com/nar/article/48/D1/D561/5624973

https://kbase.us/applist/apps/metabat/run_metabat/release?g…

https://www.perl.com/about/

www.ncbi.nlm.nih.gov

rdp.cme.msu.edu/

https://www.python.org/

drive5.com/uparse/

spades.bioinf.spbau.ru/release3.11.1/manual.html

https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471…

cgenome.net/wiki/index.php/Calypso

https://www.ebi.ac.uk/metagenomics/

https://www.genome.jp/tools/kofamkoala/

https://academic.oup.com/nar/article/46/D1/D692/4584637

exon.gatech.edu/genemarks.cgi

https://ecogenomics.github.io/CheckM/

https://github.com/jtamames/SqueezeMeta

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383904/

https://github.com/australianbiocommons

bio-bwa.sourceforge.net/

https://www.ebi.ac.uk/interpro/

https://www.hsls.pitt.edu/obrc/index.php?page=URL1144075392

https://genomebiology.biomedcentral.com/articles/10.1186/gb…

https://uni-tuebingen.de/fakultaeten/mathematisch-naturwiss…

https://github.com/bxlab/metaWRAP

www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal…

https://github.com/Adrian-Cantu/PRINSEQ-plus-plus

https://www.cbcb.umd.edu/software/metapath

exon.gatech.edu/meta_gmhmmp.cgi

https://github.com/metageni/SUPER-FOCUS

https://github.com/OpenGene/fastp

https://genome.cshlp.org/content/12/4/656

https://github.com/aquaskyline/SOAPdenovo2

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC222959/

https://github.com/facebook/rocksdb

ecogenomics.github.io/GroopM/

https://pfam.xfam.org/

metagene.nig.ac.jp/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768409/

www.pantherdb.org/data/

https://rfam.xfam.org/

https://ccb.jhu.edu/software/centrifuge/

https://pubmed.ncbi.nlm.nih.gov/22495754/

https://live.usegalaxy.eu/

eddylab.org/infernal/

https://img.jgi.doe.gov/

https://bmcbioinformatics.biomedcentral.com/articles/10.118…

https://www.elsevier.com/solutions/scopus

www.cbcb.umd.edu/software/glimmer-mg/

https://singularity.lbl.gov/

tagcleaner.sourceforge.net/

https://toolshed.g2.bx.psu.edu/view/mbernt/maxbin2/cfd50144…

https://microbiomejournal.biomedcentral.com/articles/10.118…

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933873/

https://bmcbioinformatics.biomedcentral.com/articles/10.118…

https://www.biorxiv.org/content/10.1101/2020.05.06.081778v1

https://github.com/marbl/Krona/wiki

metavelvet.dna.bio.keio.ac.jp/

https://github.com/voutcn/megahit

https://bitbucket.org/xvazquezc/otureporter/wiki/Home

https://pr2-database.org/

https://www.biorxiv.org/content/10.1101/490037v1.full.pdf

tigrfams.jcvi.org/cgi-bin/index.cgi

https://github.com/neufeld/pandaseq

https://www.ebi.ac.uk/~zerbino/velvet/

https://ccb.jhu.edu/software/kraken2/

https://digitalinsights.qiagen.com/products-overview/discov…

hannonlab.cshl.edu/fastx_toolkit/

https://github.com/dparks1134/CompareM

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117360/

www.metagenomics.wiki/tools/annotation/prokka

allie.dbcls.jp/pair/MetaORFA;Metagenomic+ORFome+Assembly.ht…

https://docs.google.com/document/d/1ytaKO9Jzg_3zaiuwERowd-9…

trna.ucsc.edu/tRNAscan-SE/

https://my.nci.org.au/mancini/ncmas/2021/

https://docs.conda.io/en/latest/

https://www.mg-rast.org/

https://www.drive5.com/usearch/manual/uchime2_algo.html

https://www.cbcb.umd.edu/software/phymm/

https://www.psort.org/psortm/

https://f1000research.com/articles/9-495

https://omics.informatics.indiana.edu/MinPath/

https://www.biorxiv.org/content/10.1101/672295v1.full

exon.gatech.edu/heuristic_gmhmmp.cgi

https://mmp.sfb.uit.no/databases/

manpages.ubuntu.com/manpages/cosmic/man1/soap.1.html

https://peerj.com/articles/425/

https://www.ebi.ac.uk/merops/

https://www.biocommons.org.au/byod-expansion

https://academic.oup.com/bioinformatics/article/34/18/3094/…

https://www.arb-silva.de/

https://sourceforge.net/projects/tax4fun2

https://ccb.jhu.edu/software/FLASH/

https://docs.google.com/document/d/1eJw2cSpoJvFAt5GhZ-h2RkY…

https://www.darwintreeoflife.org/

https://mycocosm.jgi.doe.gov/Tutorial/tutorial/kog.html

https://github.com/eggnogdb/eggnog-mapper

https://cme.h-its.org/exelixis/web/software/pear/doc.html

weizhongli-lab.org/cd-hit/

https://github.com/rrwick/Unicycler

https://mocat.embl.de/

https://benjjneb.github.io/dada2/index.html

https://drive.google.com/file/d/1TgmiFthWWjV8tQxzUZB16UunrU…

www.diamondsearch.org/index.php

https://www.genome.jp/kegg/

https://metacyc.org/

www.tcdb.org/

application.sb-roscoff.fr/cyanorak/;jsessionid=80A8351DD8C9…

https://gtdb.ecogenomic.org/

https://blast.ncbi.nlm.nih.gov/Blast.cgi

prinseq.sourceforge.net/

https://github.com/picrust/picrust2

https://usegalaxy.org.au/

https://github.com/GATB/gatb-minia-pipeline

https://www.ebi.ac.uk/metagenomics/pipelines

www.iqtree.org/

https://www.bioconductor.org/packages/release/bioc/html/met…

https://sourceforge.net/projects/metacv/

https://github.com/gjospin/PhyloSift

evomics.org/resources/software/bioinformatics-software/maff…

https://www.ebi.ac.uk/

https://github.com/torognes/vsearch

https://github.com/loneknightpy/idba

https://academic.oup.com/bioinformatics/article/36/7/2251/5…

https://aaf.edu.au/

https://www.sciencedirect.com/science/article/pii/S00222836…

https://www.drive5.com/usearch/

darlinglab.org/mauve/mauve.html

https://academic.oup.com/nar/article/46/D1/D624/4626772

https://qiime2.org/

https://multiqc.info/docs/

https://www.genome.jp/kegg/kaas/

https://www.biocommons.org.au/events/containers-intro

https://www.youtube.com/australianbiocommons

https://pubseed.theseed.org/

ER-User Guides (1) Page: Microbiome Analysis Infrastructure Roadmap V1.1