kbbq

K-mer based base quality score recalibration.

downloading, building, and installing

git clone https://github.com/adamjorr/kbbq.git
cd kbbq/
cd build/
cmake -DCMAKE_BUILD_TYPE=Release ..
cmake --build .
cmake --install .

Use the --prefix option to change where CMake installs the executable if you don't have permission to use the default:

cmake --install . --prefix ~/.local/

will put the executable in ~/.local/bin/, a common place for such things. Alternatively, move the executable to somewhere on your path or call it from the build directory.

The only dependency is HTSLib. Currently kbbq requires POSIX-compliance for posix_memalign and getopt_long. This means you may struggle to compile on Windows systems; compiling on Cygwin for Windows should be OK.

It also requires a processor that supports AVX1 instructions. If you run into a problem compiling because your processor doesn't support AVX, open an issue and I will write a workaround.

quickstart

kbbq --threads 6 --genomelen NUM_BASEPAIRS --coverage COVERAGE INPUT.fq > RECALIBRATED.fq.gz

For example, use --genomelen 1000000 --coverage 20 for a 1 megabase region sequenced to a depth of 20X. If the coverage is not provided, kbbq will take an extra pass through the data to estimate it. If the genome length is not provided, it can be estimated using the headers in a BAM file, but it will fail with FASTQ input.

kbbq accepts reads in SAM/BAM or FASTQ format, gzipped or not. It will automatically detect the format of the input. If the input is SAM/BAM, none of the alignment information is used; it is merely supported for convenience. The output will be gzipped.

options

Parameter	Short Option	Default Value	Summary
--ksize	-k	32	Size of k-mer to use for correction
--use-oq	-u	Off	Use BAM OQ tag values as quality scores
--set-oq	-s	Off	Set BAM OQ tag values before recalibration
--genomelen	-g	Estimated for BAM, required for FASTQ	The approximate size of the sequenced region in base-pairs.
--coverage	-c	Estimated from data	Approximate sequencing coverage
--fixed	-f	Off	Treat changes to reads in the given file as errors and recalibrate.
--alpha	-a	7 / coverage	Rate to sample k-mers
--threads	-t	1	Number of CPU threads to use

details

kbbq uses an error correction method similar to Lighter to find errors in whole-genome sequencing reads, then applies a hierarchical model similar to GATK's BaseRecalibrator to recalibrate quality scores.