config.txt

Project name         = AOB_chloro
Insert size          = 300
Insert size aut      = yes
Read Length          = 101
Type                 = chloro
Genome Range         = 120000-200000
K-mer                = 39
Insert Range         = 1.6
Insert Range strict  = 1.2
Single/Paired        = PE
Max memory           =
Coverage Cut off     = 1000
Extended log         = 0
Combined reads       = /path/to/reads/AOB_reads.fastq
Forward reads        = 
Reverse reads        = 
Seed Input           = Seed_AOB.fasta
Chloroplast sequence =


Project name         = Choose a name for your project, it will be used for the output files.
Insert size          = Total insert size of your paired end reads, it doesn't have to be accurate but should be close enough.
Insert size auto     = (yes/no) This will finetune your insert size automatically (Default: yes)
Read Length          = The read length of your reads.
Type                 = (chloro/mito/mito_plant) "chloro" for chloroplast assembly, "mito" for mitochondrial assembly and 
                       "mito_plant" for mitochondrial assembly in plants.
Genome Range         = (minimum genome size-maximum genome size) The expected genome size range of the genome.
                       Default value for mito: 12000-20000 / Default value for chloro: 120000-200000
                       If the expected size is know, you can lower the range, this can be useful when there is a repetitive
                       region, what could lead to a premature circularization of the genome.
K-mer                = (integer) This is the length of the overlap between matching reads (Default: 39). 
                       If reads are shorter then 90 bp or you have low coverage data, this value should be decreased down to 23. 
                       For reads longer then 101 bp, this value can be increased, but this is not necessary.
Insert Range         = This variation on the insert size, could lower it when the coverage is very high or raise it when the
                       coverage is too low (Default: 1.6). 
Insert Range strict  = Strict variation to resolve repetitive regions (Default: 1.2). 
Single/Paired        = For the moment only paired end reads are supported.
Max memory           = You can choose a max memory usage, suitable to automatically subsample the data or when you have limited                      
                       memory capacity. If you have sufficient memory, leave it blank, else write your available memory in GB
                       (if you have for example a 8 GB RAM laptop, put down 7 or 7.5 (don't add the unit in the config file))
Coverage Cut off     = You can speed up the assembly by lowering the coverage cut off, standard it will use up to 1000 coverage
Extended log         = Prints out a very extensive log, could be useful to send me when there is a problem  (0/1).
Combined reads       = The path to the file that contains the combined reads (forward and reverse in 1 file)
Forward reads        = The path to the file that contains the forward reads (not necessary when there is a merged file)
Reverse reads        = The path to the file that contains the reverse reads (not necessary when there is a merged file)
Seed Input           = The path to the file that contains the seed sequence.
Chloroplast sequence = The path to the file that contains the chloroplast sequence (Only for mito_plant mode).