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코로나-19 바이러스 발굴이나 감시에 유용한 생물정보학 리소스

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조회 190 회 작성일 21-01-09 22:51 댓글 0

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 코로나-19 바이러스 발굴이나 감시에 유용한 생물정보학 리소스(Bioinformatics resources for SARS-CoV-2 discovery and surveillance)


  Databases and software URL
Data quality control   Trimmomatic  http://www.usadellab.org/cms/index.php?page=trimmomatic 
   Cutadapt  https://cutadapt.readthedocs.io/en/stable/ 
   SOAPnuke  https://github.com/BGI-flexlab/SOAPnuke 
   AfterQC  http://www.github.com/OpenGene/AfterQC 
   Fastp*  https://github.com/OpenGene/fastp 
   Cut_Multi_Primer.py  https://github.com/MGI-tech-bioinformatics/SARS-CoV-2_Multi-PCR_v1.0 
   NanoPack  https://github.com/wdecoster/nanopack 
   Porechop  https://github.com/rrwick/Porechop 
Read mapping   Hisat2  https://daehwankimlab.github.io/hisat2/ 
   BWA  http://bio-bwa.sourceforge.net/ 
   Bowtie2*  http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 
   KMA  https://bitbucket.org/genomicepidemiology/kma 
   SortmeRNA  http://bioinfo.lifl.fr/RNA/sortmerna 
   Minimap2  https://github.com/lh3/minimap2 
   NGMLR  https://github.com/philres/ngmlr 
   MarginAlign  https://github.com/benedictpaten/marginAlign 
De novo assembly   Trinity*  http://www.nature.com/nbt/index.html. 
   Megahit  https://hku-bal.github.io/megabox/ 
   SPAdes  http://bioinf.spbau.ru/spades 
   Trans-ABySS  https://github.com/bcgsc/transabyss 
   PEHaplo  https://github.com/chjiao/PEHaplo 
   SAVAGE  https://bitbucket.org/jbaaijens/savage/src 
   coronaSPAdes  http://cab.spbu.ru/software/coronaspades/ 
Blast   Diamond*  https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/diamond/ 
   Blastn*  ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST 
   Phyre2  http://www.sbg.bio.ic.ac.uk/phyre2/html 
   Canu  https://github.com/marbl/canu 
   Falcon  https://github.com/PacificBiosciences/falcon 
   Miniasm  https://github.com/lh3/miniasm 
Genome visualization   IGV  http://software.broadinstitute.org/software/igv/ 
   Geneious*  https://www.geneious.com/ 
   QUAST  https://sourceforge.net/projects/quast/ 
   SEQMAN  https://www.dnastar.com/software/molecular-biology/ 
Database   GISAID*  https://www.epicov.org/ 
   NCBI*  https://www.ncbi.nlm.nih.gov/ 
   CNCB/NGDC database  https://bigd.big.ac.cn/ncov/ 
   Genome Warehouse (GWH)  https://bigd.big.ac.cn/gwh/ 
   Virus Pathogen Resource (ViPR)  https://www.viprbrc.org/ 
Sequence alignment   CLUSTALW  https://www.genome.jp/tools-bin/clustalw 
   MAFFT*  https://mafft.cbrc.jp/alignment/software/ 
   MUSCLE  http://drive5.com/muscle/ 
   T-Coffee  http://www.tcoffee.org/ 
   ProbCons  http://probcons.stanford.edu/ 
   PRANK  http://wasabiapp.org/software/prank/ 
   Bali-Phy  http://www.bali-phy.org/ 
   StatAlign  https://dl.acm.org/doi/10.1093/bioinformatics/btn457 
   JABAWS  http://www.jalview.org/ 
   EMBL-EBI  https://www.ebi.ac.uk/ 
   webPRANK  https://www.ebi.ac.uk/goldman-srv/webprank/ 
   Jalview  http://www.jalview.org/getdown/release/ 
   MSAViewer  http://msa.biojs.net/index.html 
   AliView  http://www.ormbunkar.se/aliview/ 
   Bioedit*  http://www.mbio.ncsu.edu/BioEdit/ 
Phylogenetic analysis   jMODELTEST  http://evomics.org/learning/phylogenetics/jmodeltest/ 
   ProtTest  http://darwin.uvigo.es/software/prottest.html 
   TempEst  http://tree.bio.ed.ac.uk/software/tempest/ 
   BIONJ  http://www.atgc-montpellier.fr/bionj/ 
   PhyML  http://www.atgc-montpellier.fr/phyml/ 
   RAxML*  http://www.exelixis-lab.org/software.html 
   IQ-TREE  http://www.iqtree.org/ 
   MrBayes  http://nbisweden.github.io/MrBayes/ 
   PhyloBayes  http://www.atgc-montpellier.fr/phylobayes/ 
   BEAST1  http://beast.community/ 
   BEAST2  http://www.beast2.org/ 
   PAUP  http://paup.csit.fsu.edu/ 
   MEGA  https://www.megasoftware.net/ 
   PhyloSuite  http://phylosuite.jushengwu.com/ 
Tree visualization   Dendroscope  http://www-ab.informatik.uni-tuebingen.de/software/dendroscope 
   FigTree*  http://tree.bio.ed.ac.uk/software/figtree/ 
   ggtree  https://yulab-smu.github.io/treedata-book/ 
   iTOL  https://itol.embl.de/ 
   Evolview  http://www.evolgenius.info/evolview 
Genomic analysis   Pangolin COVID-19 Lineage Assigner  https://pangolin.cog-uk.io/ 
   Nextstrain analysis platform*  https://nextstrain.org/ 
   Conserved Domain Database*  https://www.ncbi.nlm.nih.gov/cdd/ 
   UCSC  http://genome.ucsc.edu/ 
   GFF2PS  http://genome.imim.es/software/gfftools/GFF2PS.html 
   Vectro NTI  https://www.winsite.com/vector/vector+nti/ 
   IBS  http://ibs.biocuckoo.org/ 
   PHYLIP  https://evolution.genetics.washington.edu/phylip.html 
   SimPlot*  https://sray.med.som.jhmi.edu/SCRoftware/simplot/ 
   RDP  http://web.cbio.uct.ac.za/~darren/rdp.html 
   Swiss-Model program*  https://swissmodel.expasy.org/ 
   PyMOL*  https://www.lfd.uci.edu/~gohlke/pythonlibs/ 

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