Commit 1cb417ee authored by Raphael Müller's avatar Raphael Müller
Browse files
parents 17149463 c696c3fe
......@@ -96,15 +96,55 @@ Optional Options: [default]
## Graphical description
```mermaid
graph Backmap
graph TD;
Assembly[[Assembly]] --> BWAIndex{bwa index};
Assembly --> MinimapP{minimap2};
Assembly --> MinimapN{minimap2};
BWAI --> BWAMemSE{bwa mem};
BWAI --> BWAMemPE{bwa mem};
subgraph Illumina
BWAIndex{bwa index} --> BWAI[BWA Index Files];
SER[[Single-end Reads]] --> BWAMemSE;
PER[[Paired-end Reads]] --> BWAMemPE;
BWAMemSE --> SEBam[[Single-end Mapped Reads]] --> SMI{samtools merge};
BWAMemPE --> PEBam[[Paired-end Mapped Reads]] --> SMI{samtools merge};
SMI --> IMer[Illumina Merged Bam Files] --> SSI{samtools sort};
SSI --> ISor[Illumina Sorted Bam Files];
end
subgraph PacBio
PB[[PacBio Reads]] --> MinimapP;
MinimapP --> MBam[[Pacbio Mapped Reads]] --> SMP{samtools merge};
SMP --> PMer[Pacbio Merged Bam Files] --> SSP{samtools sort};
SSP --> PSor[Pacbio Sorted Bam Files];
end
subgraph Nanopore
ONT[[Nanopore Reads]] --> MinimapN;
MinimapN --> NBam[[Nanopore Mapped Reads]] --> SMN{samtools merge};
SMN --> NMer[Nanopore Merged Bam Files] --> SSN{samtools sort};
SSN --> NSor[Nanopore Sorted Bam Files];
end
ISor --> QMI{qualimap} --> MultiQC{{multiqc}}
PSor --> QMI
NSor --> QMI
ISor --> bedI{bedtools genomecov} --> RCovSingleI{{"R Coverage Plot (single)"}}
PSor --> bedI
NSor --> bedI
bedI --> RCovMulti{{"R Coverage Plot (multi)"}}
ISor --> SSTI{{samtools stat}}
PSor --> SSTI
NSor --> SSTI
bedI --> GSEI{{Genome Size Estimation}}
Assembly --> GSEI
Assembly --> BWAIndex[BWA Index]
Assembly --> Minimap[Minimap 2]
BWAIndex -- Index Files --> BWAMem[BWA Mem]
SER[Single-end Reads] --> BWAMem
PER[Paired-end Reads] --> BWAMem
end
```
## Changes to the original perl pipeline
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment