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)