Hitting associations with k-mers

To install HAWK run (X.Y.Z is the version)

tar xf hawk-X.Y.Z-beta.tar
cd hawk-X.Y.Z-beta
make

JELLYFISH (modified version)

ABYSS

The first step in the pipeline is to count k-mers in each sample, find total number of k-mers per sample, discard k-mers that appear once and sort the k-mers. The k-mer file contains one line per k-mer present and each line contains an integer representing the k-mer and its count separated by a space. The integer representation is given by using 0 for 'A', 1 for 'C', 2 for 'G' and 3 for 'T'.

k-mer counting can be done using a modified version of the tool JELLYFISH provided in the 'supplements' folder with HAWK. All of the steps mentioned above can be performed by installing this version of JELLYFISH and then running the script 'countKmers' in supplements with necessary modifications. This will write the names of sorted k-mer count files in 'sorted_files.txt' and total k-mer count in samples in 'total_kmers.txt'.

Copy 'sorted_files.txt' and 'total_kmers.txt' corresponding to case samples into a folder and rename them 'case_sorted_files.txt' and 'case_total_kmers.txt'. Similarly, copy 'sorted_files.txt' and 'total_kmers.txt' corresponding to control samples into the same folder and rename them 'control_sorted_files.txt' and 'control_total_kmers.txt'.

Copy the scripts 'runHawk' and 'runAbyss' into the folder and run

./runHawk
./runAbyss

The k-mers with significant association to case and controls will be in 'case_out_sig.fasta' and 'control_out_sig.fasta' and the assembled sequences will be in 'case_abyss.25_49.fasta' and 'control_abyss.25_49.fasta' respectively.

Statistics about a can be obtained by running

./kmerSummary <sequence>

This will output the following averaged over all constituent k-mers. P-value Total case count for k-mer Total control count for k-mer Number of case samples k-mer is present in Number of control samples k-mer is present in

'kmerstats.txt' will list the constituent k-mers and total counts in cases and controls, p-values and counts in individual samples.