High-speed toolkit for extracting cfDNA fragmentation features
A fast, comprehensive toolkit for computing cfDNA fragmentation features from whole-genome sequencing data. Supports a wide range of fragmentation metrics used in liquid biopsy research.
Predict cfDNA methylation and tissue-of-origin by cfDNA fragmentation patterns
FinaleMe (FragmentatIoN AnaLysis of cEll-free DNA Methylation) is a Java program to predict DNA methylation in deep and low-coverage cell-free DNA WGS data without other training data.
A browser and database of cell-free DNA fragmentation patterns
Contains thousands of uniformly processed cfDNA WGS datasets across pathological conditions. Includes a fragmentation genome browser integrated with multi-omics data.
De novo characterization of cell-free DNA fragmentation hotspots
An approach to characterize cfDNA fragmentation hotspots from whole-genome sequencing data. Useful for early-stage cancer detection and biomarker discovery.
Computational tools for Methyl-HiC and NOMe-HiC alignment
Based on the BWA aligner, Bhmem is aware of bisulfite-converted reads and genome. Handles Hi-C reads in bisulfite-converted space for joint epigenomic profiling.
Combined SNP and methylation caller for bisulfite sequencing
A GATK-based package for genotyping and DNA methylation calling in bisulfite-treated sequencing data, including Bisulfite-seq, NOMe-seq, and RRBS.