config.txt

Project:
-----------------------
Project name          = projectname
Assembly length       = 1000000
Save assembled reads  = 
Seed Input            = /path/to/seed_file/Seed.fasta
Genome size           =
Ploidy                = 2
Circular              =
Threads               = 30
Output path           = /path/to/output_folder/
TMP path              = /path/to/output_folder/TMP/

Nanopore reads:
-----------------------
Nanopore reads        = /path/to/reads/
Local DB and NP reads = /path/to/database/
Sequencing depth NP   = 
R10                   =
Min read length NP    =

PacBio reads:
-----------------------
PacBio reads          = /path/to/reads/
Local DB and PB reads = /path/to/database/
Sequencing depth PB   = 
Min read length PB    =


Project:
-----------------------
Project name          = Choose a name for your project, it will be used for the output files.
Assembly length       = If you want the assembly to terminate after a certain length, you can give the desired length; 
                        If you want to assemble the complete dataset write: "WG"
Save assembled reads  = All the reads used for the assembly will be stored in seperate files (yes/no)
Seed Input            = The path to the file that contains the seed sequence.
Genome size           = Either you give the genome size (in Gbp) or you give the sequencing depth below.
Ploidy                = Give the ploidy of the sample. If it is a very heterozygous diploid species (>2%), you can give ploidy 1
Circular              = "Yes" for when the targeted sequence is circular, make sure to give an assembly length, it will try to circularize after reaching that length
Threads               = It is strongly adviced to use multiple cores for the assembly, give here the available cores
Output path           = /path/to/output_folder/
TMP path              = /path/to/temporary_folder/

Nanopore reads:
-----------------------
Nanopore reads        = Only use this when you run the dataset for the first time. 
Local DB and NP reads = If you ran the dataset before, you can give the path of the previous output folder to reuse the database
Sequencing depth NP   = Give an estimation of the sequencing depth
R10                   = If you are using R10 data, please write "yes" here
Min read length NP    = Give the minimum read length to be used in the assembly, (default: 1000)

PacBio reads:
-----------------------
PacBio reads          = Only use this when you run the dataset for the first time. 
Local DB and NP reads = If you ran the dataset before, you can give the path of the previous output folder to reuse the database
Sequencing depth PB   = 
Min read length PB    = Give the minimum read length to be used in the assembly, (default: 500)