kmap

Standalone tool based on the bwa index to locate a set of kmers along a reference genome. klocate searches each kmer (full and perfect match) in the index and outputs all positions the kmer maps to (output to sdtout in bed format).

Download and installation

git clone --recursive https://github.com/ldenti/klocate.git
cd klocate/bwa
make
cd ../KMC
make
cd ..
make

Usage

klocate -h

klocate index -h

klocate map -h

Example

# Index the reference genome
./klocate index data/dros.4.fa

# Locate kmers from txt list (txt mode)
./klocate find -k 23 -f 0 data/dros.4.fa data/query.k23.txt > txt.bed

# Locate kmers from fasta/q file (fx mode)
./klocate find -k 23 -f 1 data/dros.4.fa data/query.k23.fa > fa.bed
./klocate find -k 23 -f 1 data/dros.4.fa data/query.k23.fq > fq.bed

# Locate kmers from KMC database (kmc mode)
./klocate find -k 23 -f 2 data/dros.4.fa data/query.k23 > kmc.bed

TODO

• extensive experimental evaluation
• kmer sequence in output bed
• option to map (k-1)-mers
• verbose mode
• test a different index (?)
• multithreading (?)