A set of utilities to calculate the median number of times the k-mers in a sequence of interest occur across the whole set. For high-quality sequencing reads, this provides a rough approximation of coverage.
The code is based on the Profex module of FastK, and is intended to be used in conjunction with FastK. Though it is possible to obtain medians by processing the standard Profex output, performing the calculations directly via the C-library interface is more efficient.
This program is based on FastK's Profex (commit 8b5b988), but returns the median count for each read in a list, instead of a full list of k-mer counts. It requires a FastK profile file as input.
Usage:
Generate a profile for a read set using FASTK:
./FastK -k<k-mer length> -p -v <file with sequences>
Then get the median counts:
./ProfMedian <profile: .prof> <read id: list of integers >= 1>
This tool performs the same calculation as ProfMedian, but iterates through the full read set in the profile.
Usage:
./ProfMedianAll <profile: .prof>
Download the files from this repository, navigate to the src directory, and run make. This will compile the programs described above, as well as the standard FastK binaries (commit f7365de).
For the original FastK Readme, see here or visit https://github.com/thegenemyers/FASTK
This repository incorporates code from multiple pieces of software, for which the terms can be found under:
- FastK: src/LICENSE
- Htslib: src/HTSLIB/LICENSE
- Libdeflate: src/LIBDEFLATE/COPYING