diff --git a/README.md b/README.md index 08916c6..672c2a9 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,8 @@ On release, automated continuous integration tests run the pipeline on a full-si +![](docs/images/taxprofiler_tube.png) + 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Performs optional read pre-processing - Adapter clipping and merging (short read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long read: [porechop](https://github.com/rrwick/Porechop)) diff --git a/docs/images/taxprofiler_tube.pdf b/docs/images/taxprofiler_tube.pdf new file mode 100644 index 0000000..63d8c06 Binary files /dev/null and b/docs/images/taxprofiler_tube.pdf differ diff --git a/docs/images/taxprofiler_tube.png b/docs/images/taxprofiler_tube.png new file mode 100644 index 0000000..0d0a4aa Binary files /dev/null and b/docs/images/taxprofiler_tube.png differ diff --git a/docs/images/taxprofiler_tube.svg b/docs/images/taxprofiler_tube.svg new file mode 100644 index 0000000..0ea3460 --- /dev/null +++ b/docs/images/taxprofiler_tube.svg @@ -0,0 +1,4407 @@ + + + +SEQUENCINGQUALITY CONTROLfastqfastqfastqfasta(ADAPTER TRIMMING & MERGING)(COMPLEXITY FILTERING)(HOST REMOVAL)(RUN MERGING)TAXONOMIC CLASSIFICATIONSUMMARY STATISTICSfastpAdapterRemovalBBDukPRINSEQ++Short ReadsAll ReadsProfileMultiple databasesLog FilesLong ReadsBowtie2catminimap2FiltlongMultiQCKronaPorechopBrackenKraken2KrakenUniqCentrifugeKaijumOTUsMetaPhlAn3MALTDIAMONDFastQCFastQCFastQC(LENGTH FILTERING)taxfindertaxprofiler/dbtsvtsvtsvtsvtsvtsvtsvtsvtsvtsvMANDATORY STEP(OPTIONAL STEP)htmlhtml