Tools

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.

We collected thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns.

We developed an approach to de novo characterize the cfDNA fragmentation hotspots from whole-genome sequencing. In healthy, cfDNA fragmentation hotspots are highly enriched in gene-regulatory elements, especially open chromatin regions from hematopoietic cells. The results highlight the significance of de novo characterizing the cell-free DNA fragmentation hotspots for detecting early-stage cancers and dissection of gene-regulatory aberrations in cancers.

Hi-C reads at bisulfite converted space are hard to be mapped. Bhmem is based on bwa aligner but aware of bisulfite converted reads and genome.

BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol.