diff --git a/docs/images/ampliseq_workflow.png b/docs/images/ampliseq_workflow.png index 80aa6d3e..3c82a179 100644 Binary files a/docs/images/ampliseq_workflow.png and b/docs/images/ampliseq_workflow.png differ diff --git a/docs/images/ampliseq_workflow.svg b/docs/images/ampliseq_workflow.svg index be64d887..5ef5bfe4 100644 --- a/docs/images/ampliseq_workflow.svg +++ b/docs/images/ampliseq_workflow.svg @@ -8,8 +8,8 @@ xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" - inkscape:export-ydpi="289.40701" - inkscape:export-xdpi="289.40701" + inkscape:export-ydpi="288.93866" + inkscape:export-xdpi="288.93866" inkscape:export-filename="/home/daniel/Desktop/github-ampliseq/ampliseq/docs/images/ampliseq_workflow.png" sodipodi:docname="ampliseq_workflow.svg" inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)" @@ -108,7 +108,7 @@ id="linearGradient5670-9" xlink:href="#linearGradient5668" inkscape:collect="always" - gradientTransform="matrix(0.26458333,0,0,0.28227707,12.561448,86.009878)" /> + gradientTransform="matrix(0.2198694,0,0,0.07790728,15.908501,81.523443)" /> + gradientTransform="matrix(0.56824703,0,0,0.09280212,79.630896,83.375459)" /> + gradientTransform="matrix(0.23505629,0,0,0.17839932,198.70657,91.35846)" /> + gradientTransform="matrix(0,-0.29133543,0.10679224,0,93.23148,181.36455)" /> + + + + + + + + + + - Primer trimming Or - Quality filtering - Evaluation + transform="translate(-33.108802,-5.9139782)"> cutadapt + x="36.110825" + y="102.96124" + style="font-size:3.17499995px;stroke-width:0.26458299">Primer trimming + transform="translate(0,-1.693077)"> cutadapt + x="3.6492712" + y="105.7519" + style="font-size:3.17499995px;stroke-width:0.26458299;text-anchor:middle;text-align:center" + id="tspan443">Read-through primer removal + transform="translate(-33.108802,4.7625029)"> filterAndTrim + x="36.867367" + y="109.48287" + style="font-size:3.17499995px;stroke-width:0.26458299">Quality filtering + transform="matrix(1,0,0,1.0159836,-33.108802,-17.485014)" + style="stroke-width:0.99210274"> FastQC - - - - Quality profileplotQualityProfile + x="47.334946" + y="103.80434" + style="font-size:3.17499995px;text-align:center;text-anchor:middle;stroke-width:0.26249352" + id="tspan469" />visualisation Infer ASVs - Remove multipleor read-throughprimers Taxonomicclassification Quality control - DADA2 - DADA2 - QIIME2 + id="tspan19050-6">Pre-processing + transform="translate(-6.5020209,-10.583356)"> assignTaxonomy - - - - addSpecies + x="105.06666" + y="107.40818" + style="font-size:3.17499995px;stroke-width:0.26458299">DADA2 + transform="translate(-1.5875,-27.976339)"> extract-reads - - - - classify-sklearn - - - - fit-classifier-naive-bayes + x="100.11958" + y="131.19937" + style="font-size:3.17499995px;stroke-width:0.26458299">QIIME2 + + + rx="3.8374953" /> Reference taxonomy + y="81.142838" + x="198.43483" + sodipodi:role="line" + id="tspan19364">Visualisation + id="g5322" + transform="translate(5.2916669,-5.4988164)"> + y="96.610046" + x="177.25598" + height="7.7119999" + width="31.516283" + id="rect4770-6-8-5-4-1-4" + style="fill:#24af63;fill-opacity:1;stroke:#000000;stroke-width:0.30000001;stroke-linecap:square;stroke-linejoin:bevel;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:normal" /> DifferentialUNITE + id="tspan5488" />abundance + id="g5499" + transform="translate(5.2916669,1.8520777)"> + y="82.049942" + x="177.25598" + height="4.9341259" + width="31.516283" + id="rect4770-6-8-5-4-1-4-30" + style="fill:#24af63;fill-opacity:1;stroke:#000000;stroke-width:0.30000001;stroke-linecap:square;stroke-linejoin:bevel;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:normal" /> GTDB + xml:space="preserve">Barplots + inkscape:export-ydpi="305.81" + inkscape:export-xdpi="305.81" + id="g4902-7" + transform="translate(56.220076,-37.391713)" + inkscape:export-filename="C:\Users\fagernaes\Pictures\eager2\eager2_workflow_review.png"> PR2 + id="tspan4772-2-5-2" + x="128.778" + y="166.49744" + style="font-size:3.17499995px;stroke-width:0.26458299">Rarefaction curves - - - SILVA - - - - RDP - - - - - Visualisation - Predict function - Differentialabundance - - ANCOM - - barplot - - PICRUSt2 - Quality control - - - alpha-rarefaction - - Alpha- & beta-diversity Reporting Visualisations,tables, formats + transform="translate(6.023189,2.6458334)"> - + transform="translate(5.2916669,-11.117278)"> qiime diversity - - - qiime diversity adonis - - Taxonomicfiltering - Abundance & prevalencefiltering - - - feature-table filter-features + sodipodi:role="line">Alpha diversity + id="g5309" + transform="translate(5.2916669,0.48736897)"> - taxa filter-table - - - + height="7.7119999" + x="177.25591" + y="115.02939" + ry="2.4670627" /> taxa filter-seqs - - Abundancetables - - - taxa collapse - - - - feature-table relative-frequency + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.17499995px;line-height:0.25;font-family:Arial;-inkscape-font-specification:Arial;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.26458299" + x="192.96909" + y="118.11877" + id="text4774-5-7-6-5-5-6">Beta diversityfeature importance + transform="translate(-36.512505,-33.082214)"> learnErrors + sodipodi:role="line">Error correction + transform="translate(-36.512505,-9.3450706)"> dada + sodipodi:role="line">Chimera removal + id="g17790" + transform="translate(-1.5875,-23.465824)"> removeBimeraDenovo + id="tspan4772-0-5-9-0" + x="50.290581" + y="146.19206" + style="font-size:3.17499995px;stroke-width:0.26458299">rRNA filtering - - Barrnap - - + id="g17790-3" + transform="translate(-1.5875,-16.418046)"> length filtering + x="49.203053" + y="146.19206" + style="font-size:3.17499995px;stroke-width:0.26458299">Length filtering (ASVs) - - mergeSequenceTables - - + transform="translate(-37.041672,0.05876586)"> ITSx + x="79.879478" + y="143.81081" + style="font-size:3.17499995px;stroke-width:0.26458299">ITS region extraction (metadata) - - cutadapt - - Extract ITS region - Filter ASVs - (metadata) mandatory - - - CO1 - + transform="translate(-1.632336,-9.3702695)"> coding region + x="44.223511" + y="146.19206" + style="font-size:3.17499995px;stroke-width:0.26458299">Coding region filtering - SINTAX + transform="translate(-1.5875,-21.284112)"> VSEARCH + x="99.841301" + y="131.48384" + style="font-size:3.17499995px;stroke-width:0.26458299">SINTAX - Phylogeneticplacement + transform="translate(-1.5875,-14.447919)"> HMMER / MAFFT - - - - PhylogeneticGappa + x="105.29136" + y="132.46269" + style="font-size:3.17499995px;text-align:center;text-anchor:middle;stroke-width:0.26458299" + id="tspan5561" />placement + transform="translate(-1.5875,-11.701769)"> EPA-NG + x="99.532791" + y="138.1176" + style="font-size:3.17499995px;stroke-width:0.26458299">Kraken2 - - - RefSeq - - - - Greengenes - - Kraken2 + transform="translate(-1.8069448,-30.513599)"> VSEARCH + x="45.290112" + y="146.19206" + style="font-size:3.17499995px;stroke-width:0.26458299">Sequence clustering Cluster OTUs + sodipodi:role="line">Post-processing - + + + Beta diversity + + + + Reference taxonomy + + + UNITE + + + + GTDB + + + + PR2 + + + + SILVA + + + + RDP + + + + CO1 + + + + RefSeq + + + + Greengenes + + + + NifH + + + + + Sidle + + Single region + Multi region + + + Filtering + + + Abundance + + + + Taxonomy + + + + Prevalence + + + + + Tables + + + Predicted functions + + + + Relative abundance + + + + Counts + + + + Aggregatedtaxonomies + + + + Sequences + + + + SBDI submission file + + + + Read count reportper sample + + + + + + tsv + + (multi-regions)