How to use MEGAN
To analyze a set of reads using MEGAN, proceed as follows.
1) Put all your reads in one fastA file and use BLASTX to compare your reads against the NCBI-nr database. (You can also use BLASTN to compare against NCBI-nt, or other variants). Here are some hints on blasting metagenomic data sets.
2) Concatenate all the resulting blast files into one large file.
3) Once you have the BLAST results, MEGAN has to import the reads and BLAST file to generate its own archive, called an RMA file. The RMA file will only be about 10-20% the size of the original input files, but will contain all your reads and the best 25 blast matches for each read. For very large datasets, this step may require a lot of memory. In this case, install MEGAN on a large memory machine (8 GB should suffice even for one terabyte of input data) and then modify the MEGAN startup script as described in the manual to allow MEGAN more memory.
Even for relatively small datasets, running on a high memory machine is recommended as this speeds up the program significantly.
4) The main computational bottle neck of the analysis is the BLAST run. This will usually be performed on a server. We recommend that the initial parsing of the resulting blast files also be performed on a server, whereas the interactive analysis can then take place on a desktop or laptop.
5) One you have computed an RMA file for your data, this data can be downloaded, e.g. onto a laptop, and then can be explored and analyzed at ease (2 GB of memory recommended).
You will find that MEGAN allows you to open many different datasets at once and produce comparisons of them.
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\n
Megan software:
\nManual.pdf (under Megan folder):
\np.8'e geldim ..
\n\n
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MEGAN MEtaGenome ANalyzer
\nfosmid: (based on bacterial F-plasmid) 40kb of random genomic DNA.
\ncosmid:
\nBAC: Bacterial Artificial Chromosome
\n\n
contig 's: set of DNA reads
\nBLAST : gene comparison tool
\n\n
LCA, COGS, GO (Gene ontology),
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\nBLAST istiyor yaninda ??
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In CAMERA 2.0, scientific developers and metagenomics researchers seamlessly collaborate to (i) wrap data-analysis software applications and heterogeneous tools as Resource Oriented Architecture (ROA) components integrating them using scientific workflows; (ii) publish and run scientific workflows via dynamically generated uniform portal interfaces; (iii) map heterogeneous workflow products to provenance and CAMERA semantic database through a transformation component, to save output data resulting from workflow runs based on this mapping; (iv) record and visualize the provenance of all workflow run-related data and processes; and (v) conduct queries across multiple workflow executions and link these workflow executions to each other through data and provenance related to these runs. Furthermore, workflows added to CAMERA also have access to a variety of physical resources for computation and data management. 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Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random \"shotgun\" approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.", "publicationTitle": "Genome Research", "publisher": "", "place": "", "date": "Mar 2007", "volume": "17", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "377-386", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Genome Res", "DOI": "10.1101/gr.5969107", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/17255551", "accessDate": "2010-11-07T22:04:15Z", "PMID": "", "PMCID": "", "ISSN": "1088-9051", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 17255551", "tags": [ { "tag": "Atlantic Ocean", "type": 1 }, { "tag": "Biodiversity", "type": 1 }, { "tag": "Computational Biology", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Genetic Variation", "type": 1 }, { "tag": "Genome", "type": 1 }, { "tag": "Genomics", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "Species Specificity", "type": 1 } ], "collections": [ "9KI6HB4F", "ZE9FBIQ2" ], "relations": {}, "dateAdded": "2010-11-07T22:04:15Z", "dateModified": "2010-11-07T22:04:15Z" } }, { "key": "I6H8HTWF", "version": 1, "library": { "type": "group", "id": 30763, "name": "metagenomics101", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomics101", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/30763/items/I6H8HTWF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomics101/items/I6H8HTWF", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/30763/items/FP653II9", "type": "application/json" } }, "meta": { "createdByUser": { "id": 25087, "username": "kemal", "name": "Kemal Aydin", "links": { "alternate": { "href": "https://www.zotero.org/kemal", "type": "text/html" } } } }, "data": { "key": "I6H8HTWF", "version": 1, "parentItem": "FP653II9", "itemType": "attachment", "linkMode": "imported_url", "title": "MEGAN - Metagenome Analysis Software — Algorithms in Bioinformatics", "accessDate": "2010-11-07T22:00:35Z", "url": "http://www-ab.informatik.uni-tuebingen.de/software/megan", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "megan.html", "md5": null, "mtime": 1289167234849, "tags": [], "relations": {}, "dateAdded": "2010-11-07T22:00:35Z", "dateModified": "2010-11-07T22:00:35Z" } }, { "key": "FP653II9", "version": 1, "library": { "type": "group", "id": 30763, "name": "metagenomics101", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomics101", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/30763/items/FP653II9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomics101/items/FP653II9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25087, "username": "kemal", "name": "Kemal Aydin", "links": { "alternate": { "href": "https://www.zotero.org/kemal", "type": "text/html" } } }, "numChildren": 4 }, "data": { "key": "FP653II9", "version": 1, "itemType": "webpage", "title": "MEGAN - Metagenome Analysis Software — Algorithms in Bioinformatics", "creators": [], "abstractNote": "", "websiteTitle": "", "websiteType": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://www-ab.informatik.uni-tuebingen.de/software/megan", "accessDate": "2010-11-07T22:00:33Z", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [], "collections": [ "9KI6HB4F", "ZE9FBIQ2" ], "relations": {}, "dateAdded": "2010-11-07T22:00:33Z", "dateModified": "2010-11-07T22:00:33Z" } }, { "key": "22ZMAIB3", "version": 1, "library": { "type": "group", "id": 30763, "name": "metagenomics101", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomics101", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/30763/items/22ZMAIB3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomics101/items/22ZMAIB3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/30763/items/877GHTQQ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 25087, "username": "kemal", "name": "Kemal Aydin", "links": { "alternate": { "href": "https://www.zotero.org/kemal", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "22ZMAIB3", "version": 1, "parentItem": "877GHTQQ", "itemType": "note", "note": "notes:
\nbagirsaklardaki farkli bakteri kulturu sismanlik yapabiliyor, fare ornegi
\nDunyadaki fotosentezin yarisini bakteriler yapiyor..! cogu okyanuslarda yasiyor..
\nbakteriler mahir kimyagerler
\nuygulamalar:
\n", "tags": [], "relations": {}, "dateAdded": "2010-11-07T21:22:16Z", "dateModified": "2010-11-07T21:35:33Z" } }, { "key": "877GHTQQ", "version": 1, "library": { "type": "group", "id": 30763, "name": "metagenomics101", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomics101", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/30763/items/877GHTQQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomics101/items/877GHTQQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25087, "username": "kemal", "name": "Kemal Aydin", "links": { "alternate": { "href": "https://www.zotero.org/kemal", "type": "text/html" } } }, "numChildren": 2 }, "data": { "key": "877GHTQQ", "version": 1, "itemType": "webpage", "title": "Understanding Our Microbial Planet", "creators": [], "abstractNote": "", "websiteTitle": "", "websiteType": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://dels-old.nas.edu/metagenomics/", "accessDate": "2010-11-07T21:17:45Z", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2010-11-07T21:17:45Z", "dateModified": "2010-11-07T21:23:55Z" } }, { "key": "MRGG4W3N", "version": 1, "library": { "type": "group", "id": 30763, "name": "metagenomics101", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomics101", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/30763/items/MRGG4W3N", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomics101/items/MRGG4W3N", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/30763/items/877GHTQQ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 25087, "username": "kemal", "name": "Kemal Aydin", "links": { "alternate": { "href": "https://www.zotero.org/kemal", "type": "text/html" } } } }, "data": { "key": "MRGG4W3N", "version": 1, "parentItem": "877GHTQQ", "itemType": "attachment", "linkMode": "imported_url", "title": "Metagenomics", "accessDate": "2010-11-07T21:17:46Z", "url": "http://dels-old.nas.edu/metagenomics/", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "metagenomics.html", "md5": null, "mtime": 1289164666974, "tags": [], "relations": {}, "dateAdded": "2010-11-07T21:17:46Z", "dateModified": "2010-11-07T21:23:17Z" } }, { "key": "FUF7UDJT", "version": 1, "library": { "type": "group", "id": 30763, "name": "metagenomics101", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomics101", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/30763/items/FUF7UDJT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomics101/items/FUF7UDJT", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/30763/items/3HITTGNH", "type": "application/json" } }, "meta": { "createdByUser": { "id": 25087, "username": "kemal", "name": "Kemal Aydin", "links": { "alternate": { "href": "https://www.zotero.org/kemal", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "FUF7UDJT", "version": 1, "parentItem": "3HITTGNH", "itemType": "note", "note": "
summary:
\nGenomic study of uncultured microorganisms.
\nvolumnious , noisy, often partial data
\nhuman body: 10^13 cells, 10^14 bacterial cells
", "tags": [], "relations": {}, "dateAdded": "2010-11-07T17:27:34Z", "dateModified": "2010-11-07T17:30:07Z" } } ]