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--- metagenomics [2019/04/05 14:04] – [Useful papers and websites] hyjeong
+++ metagenomics [2022/07/07 10:30] (current) – ↷ Links adapted because of a move operation 207.46.13.204
@@ Line 6: / Line 6: @@
   * [[http://2017-ucsc-metagenomics.readthedocs.io/en/latest/index.html|2017 Metagenomics workshop at UC Santa Cruz]]
   * [[http://www.metagenomics.wiki/|Metagenomics wiki]]
-  * [[https://www.youtube.com/watch?v=nWeRN2lKIto|Microbiome/Metagenome Analysis Workshop: QIIME]]
+  * [[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.
+  * [[https://youtu.be/ED8VkMLYTTI|Aligning 16S sequences to reference set and filtering the alignment]] This tutorial explains how to align 16S sequences to the Silva reference set and how to filter the alignment and remove identical sequences.
 ===== 16S rRNA-based =====
 ==== QiiME ====
   * 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]]
+  * [[https://www.youtube.com/watch?v=nWeRN2lKIto|Microbiome/Metagenome Analysis Workshop: QIIME]]
   * [[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]]
@@ Line 19: / Line 21: @@
   * [[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]]
+==== Mothur ====
+  * https://www.mothur.org/ - download, wick, forum & facebook
+==== Others ====
+  * [[16S rRNA sequencing data types]]
+  * [[custom scripts for 16S rRNA sequence analysis]]
 ===== Taxonomic profiling from metagenomic shotgun sequences (without assembly) ====
@@ Line 42: / Line 48: @@
 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.
   * 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 =====
@@ Line 67: / Line 74: @@
 GroopM, a companion of CheckM, can be used to recover genomes from metagenomic data.[[https://peerj.com/articles/603/|논문]]
+===== Shotgun metagenomic analysis 2022 =====
+최근 들어서 입수한 메타게놈 자료의 분석을 위하여 새롭게 글 작성을 시작한다. 오래 전에 작성했던 위 내용의 해당 섹션을 보충하느니 차라리 새로운 섹션을 만들고, 필요하다면 별도의 위키 문서로 독립하는 것이 나을 것이다. Biostars에 실린 최근 질문과 답변(2022년 1월 20일 기준 4개월 전)이 훌륭한 시작점이 될 것이다.
+[[https://www.biostars.org/p/9488577/|Any suggestions on metagenomic pipelines for processing shotgun metagenomics whole genome sequencing samples?]] - metaWRAP, bioBakery & anvi'o
+Shotgun metagenomic analysis라고 하여 반드시 MAG(metagenome-assembled genome)을 중간물로 사용하는 것은 아니다. 예를 들어 마커 유전자 DB를 이용한 정밀한 phylogenetic analysis라면, read를 꼭 조립해야 하는 것은 아니기 때문이다.
+[[metagenomic_data_assembly_pipeline]]