| 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 | |
| Export As: | Word · PDF | |
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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/
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https://www.biocommons.org.au/byod-expansion
https://academic.oup.com/bioinformatics/article/34/18/3094/…
https://www.arb-silva.de/
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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/
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ER-User Guides (1)
Microbiome Analysis Infrastructure Roadmap V1.1
|