A collection of Rust tools to speed up the python based functionality of the CapCruncher project. Python binding have been generated to allow for easy integration into the existing python code base.
This tool takes paired FASTQ files and removes any duplicate fragments.
capcruncher-tools fastq-deduplicate -1 <input1.fastq> -2 <input2.fastq> -o <output_prefix>
This tool takes a FASTA file and a list of restriction enzymes and produces a list of fragments in BED format.
capcruncher-tools digest-genome -i <input.fasta> -o <output.bed> -r <recognition site> -p <number of threads>
This tool counts the number of interactions between a fragment (in silico digested read).
capcruncher-tools count <reporters> -f <fragments.bed> -v <viewpoints_path.bed> -o <output.hdf5> -p <number of threads>
FAQs
Extra utilities to enhance CapCruncher
We found that capcruncher-tools demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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