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 available in supplements)
EIGENSTRAT (modified version available in supplements)
R (with foreach and doParallel packages)
ABYSS
GNU sort with parallel support
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 in samples 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.
The version provided assumes reads from each sample is in a separate directory
and prefixes of all directories containing reads is Reads. For example reads from
sample1, sample 2, etc. could be in directories named Reads_sample1, Reads_sample2, etc.
It also assumes that the read files are gzipped and have extensions fastq.gz. If the read files
are not gzipped please change the zcat *.fastq.gz to cat *.fastq in line 21 in countKmers.
This will write the names of sorted k-mer count files in 'sorted_files.txt' and total k-mer count in samples in 'total_kmer_counts.txt'.
Copy 'sorted_files.txt' and 'total_kmer_counts.txt' corresponding to the samples into a folder as well as a file named 'gwas_info.txt' containing three columns separated by tabs giving a sample ID, male/female/unknown denoted by M/F/U and Case/Control status of the sample for each sample. For example
SRR3050845 U Control
SRR3050846 U Case
SRR3050847 U Control
Copy the scripts 'runHawk' and 'runAbyss' into the folder and run
./runHawk
The k-mers with significant association to case and controls will be in 'case_kmers.fasta' and 'control_kmers.fasta' which can then be assembled by running
./runAbyss
The assembled sequences will be in 'case_abyss.25_49.fasta' and 'control_abyss.25_49.fasta' respectively.