In the folder simu there is another NF pipeline for simulating reads starting from vector sequences. It is basically a wrapper of wgsim tool adapted to generate sequence from circular genomes. In the folder examples there are some inserted genes and vectors.
| parameter name | value |
|---|---|
| seqs | "$baseDir/../test/vectors/*.fa" |
| fold | 3000 |
| outerd | 600 |
| stdev | 100 |
| size | 300 |
| output | output |
| email for notification | yourmail@yourdomain |
Fasta sequences with vectors.
Number of time that the vector should be covered by the reads.
Outer read distance.
Standard deviation of the outer read distance
Output folder
Mail address for receiving a mail once the process is finished / crashed.
nextflow run simulate/simulate.nf
nextflow run main.nf