Major - Parameter "Running mode":
- Modify value "Error Correction and Assembly" to "Error correction and assembly".
- Modify the parameter description:
By default, SPAdes performs both read error correction and assembly. You can select leave one of only (corresponds to --only-assembler, --only-error-correction). Error correction is performed using BayesHammer module in case of Illumina input reads and IonHammer in case of IonTorrent data. Note that you should not use error correction in case input reads do not have quality information (e. g. FASTA input files are provided).
- Parameter "Dataset type":
- Modify values in the combo box. Replace "Multi Cell" by "Standard isolate", replace "Single Cell" by "MDA single-cell".
- Modify the description:
Select the input dataset type: standard isolate (the default value) or multiple displacement amplification (corresponds to --sc).
- Parameter "K-mers":
- Use "Auto" instead of "auto".
- Parameter "Memory limit":
- Remove " (GB)" from the parameter name. Add "Gb" to the spin box.
- Modify description of the element in the Property Editor:
In general, SPAdes (St. Petersburg genome assembler) is an assembly toolkit containing various assembly pipelines. This workflow element provides GUI for the main SPAdes executable script. One can specify Illumina, IonTorrent or PacBio reads as input. Hybrid assemblies are also possible, for example, with Oxford Nanopore or Sanger reads. To use the element, configure the type of input in the "Input data" parameter. The corresponding input ports will appear on the element. Provide URL(s) to the corresponding FASTA or FASTQ file(s) to these ports.
- Modify description of the element on the WD scene:
Assemble de novo the input data into contigs and scaffolds.