Fungal ITS meeting presentation
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PhyloSift is a metagenomic analysis tool that provides: - Support for paired-end Illumina data and marker genes for bacteria, archaea, eukaryotes, and viruses. - Taxonomy assignments based on probability distributions over a reference phylogeny. - Tools for building marker gene packages, simulating metagenomic data, placing environmental sequences on trees, and updating reference databases with new genomes. - The ability to work with any marker genes, including fungal ITS sequences if provided a reference dataset.
Fungal ITS meeting presentation
- 1. Metagenomic+tools+for+the+ fungal+community+ Holly+Bik,+UC+Davis+ 19+October+2012+
- 3. Explicitly+PhylogeneLc+Approaches+ Aligned+ EvoluLonary+ environmental+ Placement+of+ sequences+ short+reads+ ++++ Guide+Tree+
- 4. We+provide:+ ≒ Support+for+Paired+End+(raw)+Illumina+data+ ≒ Marker+gene+data+for+Bacteria,+Archaea,+ Eukaryotes,+Viruses+ ≒ Taxonomy+assignments+based+on+probability+ distribuLons+over+a+reference+phylogeny+ ≒ Complement+to+exisLng+tools++QIIME/VAMPs+ Inputs/outputs+will+be+compaLble+for+use+with+ other+soEware+tools+
- 5. Markers+ ≒ PMPROK++Dongying+Wus+Bac/Arch+markers+ ≒ EukaryoLc+Orthologs++Parfrey+2011+paper+ ≒ 16S/18S+rRNA++ ≒ Mitochondria+_+protein_coding+genes+ ≒ Viral+Markers++Markov+clustering+on+genomes+ ≒ Codon+Subtrees++鍖ner+scale+taxonomy+ ≒ Extended+Markers++plasLds,+gene+families+
- 8. 壊沿艶界庄鍖e糸&#恰27;永禽&#恰27;界顎岳看鍖仰&#恰27;(艶.乙.&#恰27;99%)&#恰27;&#恰27; Quan?ta?ve'metric'(minimum' Tree Reconcile'NCBI'taxonomy'IDs' The+Monkey++Build+Marker+Packages+ hamming'distance)'used'to'match' Reconciliation with'phylogene?c'topology' edges'between'NCBI'taxon'tree' and'molecular'phylogeny' Clean'and'package'new'marker'genes' Built Marker New'marker'gene'packages'placed'into' Packages shared'PhyloSiS'marker'directory' Mapping'File' PD' Alignment'File' Execute'index'mode' (sequence'name,'NCBI'taxon'ID)' cuto鍖' (Marker'sequences'in'FASTA'format)' Locally'indexed'marker'packages' will'not'interfere'with'automa?c' Index Marker Indexes'the'marker'databases'needed' NOTE:'New'marker'packages'are' for'LAST'and'Bow?e' named'according'to'input'鍖lenames' Execute'build_marker'mode' updates'to'PhyloSiS'core'markers' Database (e.g.'MarkerAlignment.fasta).'Core' marker'data'will'be'overwriXen' during'new'marker'builds'if'input' hmmbuild Create'pro鍖le'HMMs'(or'CMs'for' 鍖les'do'not'have'unique'names' rRNA'data)'using'input'sequences' (ssu-build) compared'to'exis?ng'PhyloSiS' markers.' Built'PhyloSiS'Marker'package' Generate'unique'IDs'for'input'sequences' Build'tree'and'collapse' Tree' HMM'pro鍖le'' FastTree topology'according'to'a'userM (CMs'for'rRNA)' 壊沿艶界庄鍖e糸&#恰27;永禽&#恰27;界顎岳看鍖仰&#恰27;(艶.乙.&#恰27;99%)&#恰27;&#恰27; Representa?ve' Taxon'map' Quan?ta?ve'metric'(minimum' sequences' hamming'distance)'used'to'match' Tree Reconcile'NCBI'taxonomy'IDs' Reconciliation with'phylogene?c'topology' edges'between'NCBI'taxon'tree' and'molecular'phylogeny' Alignment' Clean'and'package'new'marker'genes' Built Marker New'marker'gene'packages'placed'into' Packages shared'PhyloSiS'marker'directory' Execute'index'mode' Locally'indexed'marker'packages' will'not'interfere'with'automa?c' Index Marker Indexes'the'marker'databases'needed' Database for'LAST'and'Bow?e' updates'to'PhyloSiS'core'markers' Built'PhyloSiS'Marker'package'
- 9. 意鞄艶+悪温稼乙温姻看看++皆庄馨顎鉛温晦看稼+禽温岳温+ Genome&Directory& De鍖ne&the&number&of&&genomes&to&pick&(default&=&10)&and&number&of& reads&to&generate&per&鍖le&(default&=&100,000)& Execute&sim&mode& Determines&PD&contribuFons&for&taxa& PD on present&in&concatenated&guide&tree& concatenated tree in&PhyloSiH&marker&directory& Two&separate&approaches&used:& 1. Select&some&number&of&taxa&that&contribute& Select Taxa to&PD&(user&input,&default&=&10&taxa)& 2. Sample&taxa&uniformly&without&replacement& Compute metrics Calculated&metrics&include:&the&distance&to& between target and nearest&neighbors,&connecFng&branch& remaining taxa lengths,&and&the&number&of&sampled&nodes& within&various&PD&units&of&connecFng&nodes.& Knockout Work鍖ow&plugs&into&updateDB&to& remove&genomes&which&have&been&used& Swaths of Taxa to&simulate&metagenome&data,&as&well&as& a&swath&of&related&taxa.& Grinder&algorithm&randomly&generates& Generated reads&from&selected&genomes,&outputs& Simulated Reads simulated&PEAIllumina&and&454&datasets& A&new&marker&directory&is&created,& Simulation where&simulated&genomes&have&been& Marker Directory knocked&out&from&marker&packages.&&
- 10. 禽京顎沿糸温岳艶++珂庄稼庄稼乙+稼艶敬+乙艶稼看馨艶壊+ EBI' Private' NCBI' JGI' Genomes' Genomes' Genomes' Genomes' Execute' phylosi/_dbupdate.pl' Run PhyloSift (search + align) Add'new'sequences'to'marker'packages' Infer Updated Tree Amino Acid Nucleotide Tree Tree PD'metric'used'to'split'guide'tree'into' A'taxa'set'is'selected'with'a' Codon smaller'subtrees;'subsets'of'taxa'are' maxPD'cuto鍖'of'0.02'and'a'new' Prune Tree tree'is'inferred' Subtrees selected'such'that'no'branch'connecEng' them'has'length'>0.X'for'some'value'of'X' New'sequences'added'at'0.25'PD'for'amino' acid'tree;'higher'PD'threshold'enables' Update reference more'aggressive'searches'of'reference' sequences with database,'since'LAST'searching'is'faster' new data with'fewer'sequences.' Reconcile'NCBI'taxonomy'IDs'with' Tree phylogeneEc'topologies,'for'both' Reconciliation amino'acid'tree'and'codon'subtrees' Package Markers Automated Users'local'marker'databases'are'automaEcally' Download to scanned'each'Eme'PhyloSi/'is'run'and'any'new' PhyloSift Users updates'are'automaEcally'downloaded'if'available'
- 11. Tree+ReconciliaLon+in+PhyloSiE+ Environmental, Named, Sequences, Taxa,
- 13. Great!,, Not,Bad,, Ge9ng,Tricky,,
- 15. Chemoautotrophic+ Marine+ bacteria++oxidize+ Metagenome+ ammonia+into+nitrite+ Alveolate+ProLsts+ Common+seawater+ Archaea+
- 18. Marine+ Metagenome+ Tree+Placement+ Sing+Tree+_+Guppy+
- 19. Linking+with+the+Fungal+ITS+community+ ≒ How+does+fungal+ITS+sequence+data+relate+to+your+ project?+ PhyloSiE+has+the+capability+to+add+any+marker+gene+ reference+packages+that+are+relevant+for+speci鍖c+ taxonomic+communiLes++ ≒ What+fungal+ITS+data+does+your+project+currently+ provide+ None++but+we+do+mine+other+marker+genes+from+ fungal+genomes+ ≒ What+fungal+ITS+data+is+your+project+hoping+to+ provide?+ We+wouldnt+provide+data,+but+can+work+with+users+to+ increase+support+for+fungal+analyses+
- 20. Linking+with+the+Fungal+ITS+community+ ≒ Is+your+project+involved+with+curaLng+fungal+ITS+ sequences+ No,+but+we+would+curate+alignments+and+marker+ packages+of+ITS+sequences+mined+from+public+ databases+ ≒ If+so,+what+curaLon+strategies+are+being+ implemented+for+your+project?+ Alignment+鍖ltering+and+masking,+pruning+reference+ trees+ ≒ What+tools+for+working+with+fungal+ITS+sequences+ does+your+project+currently+provide?++ None+so+far++but+can+be+implemented+if+given+a+ reference+dataset+(e.g.+alignment)+
- 21. Linking+with+the+Fungal+ITS+community+ ≒ What+tools+are+you+developing+/+planning+to+ develop?++ Current+focus+is+on+mulLsample+comparisons+ Gene+tree+reconciliaLon+ Probability+distribuLon+over+tree+topology+to+ delimit+OTUs+(PhylogeneLc+OTUs)+ ≒ What+framework+of+fungal+taxonomy+does+ your+project+use?++ NCBI_derived+taxonomy+(because+of+tree+ mapping/reconciliaLon+issues)+
- 22. SATELLITE MEETING Eukaryotic Metagenomics March/April 2013 UC Davis
- 23. Acknowledgements+ UC+Davis+ ≒ Jonathan+Eisen+ ≒ Aaron+Darling+ ≒ Guillaume+Jospin+ ≒ Dongying+Wu+ ≒ David+Coil+ + PhyloSiE+SoEware+Development+on+Github:+ hAps://github.com/gjospin/PhyloSiE+ + Google+Group+for+user+support:++ hAps://groups.google.com/d/forum/phylosiE+ + TwiAer:+@PhyloSiE+