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metagenomics [2018/04/06 10:40]
hyjeong [Phylogenetic classification of contigs]
metagenomics [2019/04/23 15:52] (current)
hyjeong [Mothur]
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 ====== Haeyoung'​s metagenomics resource ====== ====== Haeyoung'​s metagenomics resource ======
-===== Useful papers ​and websites =====+===== Useful paperswebsites, and videos ​=====
   * [[https://​www.ncbi.nlm.nih.gov/​pmc/​articles/​PMC4059276/​|An introduction to the analysis of shotgun metagenomic data (Front. Plant Sci. (2014)]]   * [[https://​www.ncbi.nlm.nih.gov/​pmc/​articles/​PMC4059276/​|An introduction to the analysis of shotgun metagenomic data (Front. Plant Sci. (2014)]]
   * [[https://​www.ncbi.nlm.nih.gov/​pubmed/​28898207|Shotgun metagenomics,​ from sampling to analysis. Nature Biotechnol. (2017)]]   * [[https://​www.ncbi.nlm.nih.gov/​pubmed/​28898207|Shotgun metagenomics,​ from sampling to analysis. Nature Biotechnol. (2017)]]
   * [[http://​metagenomics-workshop.readthedocs.io/​en/​latest/​index.html|Metagenomic Workshop in Uppsala]]   * [[http://​metagenomics-workshop.readthedocs.io/​en/​latest/​index.html|Metagenomic Workshop in Uppsala]]
   * [[http://​2017-ucsc-metagenomics.readthedocs.io/​en/​latest/​index.html|2017 Metagenomics workshop at UC Santa Cruz]]   * [[http://​2017-ucsc-metagenomics.readthedocs.io/​en/​latest/​index.html|2017 Metagenomics workshop at UC Santa Cruz]]
 +  * [[http://​www.metagenomics.wiki/​|Metagenomics wiki]]
 +  * [[http://​blog.mothur.org/​2016/​01/​12/​mothur-and-qiime/​|mothur and QIIME]] Despite their differences in philosophy, //most// of the differences in mothur and QIIME are cosmetic.
  
 ===== 16S rRNA-based ===== ===== 16S rRNA-based =====
 ==== QiiME ==== ==== QiiME ====
   * http://​qiime.org/​ - no longer supported since January 1, 2018.   * http://​qiime.org/​ - no longer supported since January 1, 2018.
-  * [[https://​qiime2.org/​Qiime 2]]+  * [[https://docs.qiime2.org/2019.1/}Qiime 2 user documentation]]
   * [[http://​qiime.org/​tutorials/​index.html|Qiime official tutorial]]   * [[http://​qiime.org/​tutorials/​index.html|Qiime official tutorial]]
 +  * [[https://​www.youtube.com/​watch?​v=nWeRN2lKIto|Microbiome/​Metagenome Analysis Workshop: QIIME]]
   * [[https://​github.com/​haruosuz/​qiime|Qiime tutorial project]] **강력 추천**   * [[https://​github.com/​haruosuz/​qiime|Qiime tutorial project]] **강력 추천**
   * [[https://​docs.qiime2.org/​2017.10/​tutorials/​moving-pictures/​|Qiime 2 "​Moving Pictures"​ tutorial]] -  Caporaso의 [[https://​www.ncbi.nlm.nih.gov/​pubmed/​21624126|Genome Biol. (2011) 논문]]   * [[https://​docs.qiime2.org/​2017.10/​tutorials/​moving-pictures/​|Qiime 2 "​Moving Pictures"​ tutorial]] -  Caporaso의 [[https://​www.ncbi.nlm.nih.gov/​pubmed/​21624126|Genome Biol. (2011) 논문]]
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   * [[http://​journals.plos.org/​plosone/​article?​id=10.1371/​journal.pone.0061217|PLoS One (2013) 논문]] "​Handling and analysis of high-throughput microbiome census data"   * [[http://​journals.plos.org/​plosone/​article?​id=10.1371/​journal.pone.0061217|PLoS One (2013) 논문]] "​Handling and analysis of high-throughput microbiome census data"
   * [[http://​bioconductor.org/​packages/​release/​bioc/​html/​phyloseq.html|BioConductor]]   * [[http://​bioconductor.org/​packages/​release/​bioc/​html/​phyloseq.html|BioConductor]]
 +==== Mothur ==== 
 +  * https://​www.mothur.org/​ - download, wick, forum & facebook
 ===== Taxonomic profiling from metagenomic shotgun sequences (without assembly) ==== ===== Taxonomic profiling from metagenomic shotgun sequences (without assembly) ====
  
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 CONCOCT, MaxBin, metaBAT... CONCOCT, MaxBin, metaBAT...
  
-===== Pipelines for metagenomc data analysis =====+===== Pipelines ​or web servers ​for metagenomc data analysis =====
   * MetAMOS [[https://​github.com/​marbl/​metAMOS|GitHub]] 2016년도에는 관심이 꽤 많았었는데 요즘은 그저 그런 상태임.   * MetAMOS [[https://​github.com/​marbl/​metAMOS|GitHub]] 2016년도에는 관심이 꽤 많았었는데 요즘은 그저 그런 상태임.
   * MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis [[https://​www.biorxiv.org/​content/​early/​2018/​03/​06/​277442|bioRxiv]] [[https://​github.com/​bxlab/​metaWRAP|GitHub]]   * MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis [[https://​www.biorxiv.org/​content/​early/​2018/​03/​06/​277442|bioRxiv]] [[https://​github.com/​bxlab/​metaWRAP|GitHub]]
 +  * MicrobiomeAnalysis - a web-based tool for comprehensive statistical,​ visual and meta-analysis of microbiome data https://​www.microbiomeanalyst.ca/​
  
 ===== A real example of Cyanobacterial genome assembly ===== ===== A real example of Cyanobacterial genome assembly =====
metagenomics.1522978819.txt.gz · Last modified: 2018/04/06 10:40 by hyjeong