Batch function

Since NOVOPlasty3.0, it is possible to run different samples as a batch.

1. Create a batch file

First make a text file that contains all the variable parameters of the config file.
The "Project name" parameter should always be changed. Any additional parameter can be added to this file.

Below is an example of a batch file for three runs. Each run has different seed files and Illumina files.

Project1
/path/to/seed_file/Seed1.fasta
/path/to/reads/reads_1a.fastq
/path/to/reads/reads_2a.fastq
Project2
/path/to/seed_file/Seed2.fasta
/path/to/reads/reads_1b.fastq
/path/to/reads/reads_2b.fastq
Project3
/path/to/seed_file/Seed3.fasta
/path/to/reads/reads_1c.fastq
/path/to/reads/reads_2c.fastq

2. Modify your config file

The configuration file should be changed as below:

Project name line should start with "batch:" followed with the path to your batch file. Then you replace each parameter that needs to be changed for each run by "batch". Make sure this corresponds to the previous made batch file.

Project:
-----------------------
Project name          = batch:/path/to/batch_file.txt
Type                  = mito
Genome Range          = 12000-20500
K-mer                 = 39
Max memory            = 11
Extended log          =
Save assembled reads  =
Seed Input            = batch
Reference sequence    =
Variance detection    = 
Chloroplast sequence  =

Dataset 1:
-----------------------
Read Length           = 151
Insert size           = 412
Platform              = illumina
Single/Paired         = PE
Combined reads        = 
Forward reads         = batch
Reverse reads         = batch

Heteroplasmy:
-----------------------
MAF                   = 
HP exclude list       = 
PCR-free              = 

Optional:
-----------------------
Insert size auto      = yes
Insert Range          = 1.9
Insert Range strict   = 1.3
Use Quality Scores    = no