Reference genome FASTA file

Output files base string

Number of threads for those steps that support multithreading

Genome label is used by web-ui to show label

Tab-separated annotation file

Genome details

Ribosomal DNA sequence FASTA file

Genome description is used by web-ui to show description

default: 1

int>0: suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction

Mitochondrial chromosome sequence FASTA file

Annotation input file

MACS2 effective genome size: hs, mm, ce, dm or number, for example 2.7e9

If you are using a genome with a large (>5,000) number of references (chrosomes/scaffolds), you may need to reduce the --genomeChrBinNbits to reduce RAM consumption. The following scaling is recommended: --genomeChrBinNbits = min(18,log2[max(GenomeLength/NumberOfReferences,ReadLength)]). For example, for 3 gigaBase genome with 100,000 chromosomes/scaffolds, this is equal to 15.

default: 18

int: =log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins. For a genome with large number of contigs, it is recommended to scale this parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]).

For small genomes, the parameter --genomeSAindexNbases must to be scaled down, with a typical value of min(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome, this is equal to 9, for 100 kiloBase genome, this is equal to 7.

default: 14

int: length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter –genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1).

31000000000 int>0: maximum available RAM (bytes) for genome generation

For small genomes, the parameter --genomeSAindexNbases must to be scaled down, with a typical value of min(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome, this is equal to 9, for 100 kiloBase genome, this is equal to 7.

default: 14

int: length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter –genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1).