Submit Computation Job

Format for Advanced Parameter Settings:

- .txt files

Requirements

Parameter file requirements:

• Each species needs at least ONE of (genmap OR macle) parameters
• You can provide only genmap, only macle, or both
• Dups parameters are completely optional
• Automatic parameters are generated for any species missing both genmap and macle

Example scenarios:
✓ Upload only genmap.txt (macle auto-generated for species not in genmap.txt)
✓ Upload only macle.txt (genmap auto-generated for species not in macle.txt)
✓ Upload both genmap.txt and macle.txt
✓ Upload genmap.txt + dups.txt (macle auto-generated, dups optional)
✓ Upload nothing (all parameters auto-generated)

For all

Please provide line-separated files with a set of parameters according to the descriptions below. In short: genmap corresponds to filtering based on k-mer counting done with GenMap; macle corresponds to filtering done with macle, a tool to compute the match complexity; dups corresponds to identification of potential duplicates with the help of using longer k-mers with allowed errors for the detection of sequences with only few duplicates

At https://link.springer.com/article/10.1186/s13015-025-00275-9 the main paper describing the method can be found with a detailed description of the use of GenMap. The use of macle and the duplicate finding algorithm are subjects of the paper this webserver will be part of but a sufficient explanation is given below. If in doubt, dont use the duplicate finding mechanism. The macle tool is available on github and the parameters of window size and pitch should be straight forward.

genmap

The line is formatted like (whitespace in between):
genome k e w p s b
genome: filename without suffix (my_genome NOT my_genome.fa/fna/fasta)
k: k of k-mer counts
e: errors allowed in k-mer counting
w: size of initially overlapping windows
p: pitch of w-windows
s: (minimal) percentage of genome size of initially overlapping windows to process
b: value which one of [0,1]. 0 - take all windows. 1 - take only the ones overlapping with others from other genmap or macle filtering settings.

macle

The line is formatted like (whitespace in between):
genome w p s b
genome: filename without suffix (my_genome NOT my_genome.fa/fna/fasta)
w: size of initially overlapping windows
p: pitch of w-windows
s: (minimal) percentage of genome size of initially overlapping windows to process
b: value which one of [0,1]. 0 - take all windows. 1 - take only the ones overlapping with others from other genmap or macle filtering settings.

dups

The line is formatted like (whitespace in between):
genome k1 e1 k2 e2 w p x1 y1 x2 y2
genome: filename without suffix (my_genome NOT my_genome.fa/fna/fasta)
k1: k of k-mer counts for initial identification of candidate windows
e1: errors allowed in k1-mer counting
k2: k of k-mer counts for exclusion of windows according to x2 and y2
e2: errors allowed in k2-mer counting
w: size of initially overlapping windows
p: pitch of w-windows
x1: how many counts of initial windows are allowed (will be a range [2,x1])
y1: percentage of counts in candidate windows adhering to count values defined with x1
x2: how many counts of k2,e2-mers are regarded as indicative of bad window (and all bigger than x2)
y2: percentage of counts in candidate windows from which candidate is discarded if x2 count larger than to y2