polyploid-potato-assembly

Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data"

1. Dosage estimation of the nodes in the hifiasm assembly graph:

run snakemake in the coverage-analysis directory. Requires minimap2 and samtools.

2. K-mer analysis:

Installation:

Note: Requires an installation of the jellyfish package. If not installed yet, you can install it via conda install jellyfish

git clone git@github.com:rebeccaserramari/polyploid-potato-assembly.git

cd polyploid-potato-assembly/kmer-counting

mkdir build; cd build; cmake ..; make

Running k-mer counting procedure

1. To run the full procedure, including finding unique k-mers in <targetfile>, counting the found unique k-mers in a set of sequences samples, and merging the resulting files:

   run snakemake within the kmer-counting directory.

Make sure to update the config files accordingly!
2. To run the first step individually, i.e. find k-mers of length <len> that are uniquely present in <targetfile> and not in <comparisonfile>:

`./polyassembly_findkmers find_kmers -r <targetfile> -s <comparisonfile> -k <kmerfile> -l <len>`

The resulting k-mers are stored in <kmerfile>.

3. To run the second step individually, i.e. count the unique k-mers in <samplefile>:

   /polyassembly_findkmers count_kmers -s <samplefile> -k <kmerfile> -c <output> -l <len>

3. Phased clustering

To run the full clustering procedure:

run snakemake in the cluster-phasing directory.