Welcome to AdamaJava

The project is being hosted on github.

While the repository contains code for dozens of utilities, the list below shows tools that are considered robust enough to be released for general use. Most are written in Java and require version 21. Some tools have dependencies on other software.

• qbamfilter - filters records from a BAM file
• qbasepileup - base pileups
• qcnv - a pre-processor for copy number variant (CNV) calling
• qcoverage - calculates read depth statistics for a mapped BAM
• qmito - metrics for mitochondrial sequencing
• qmotif - search BAM file records for base motifs
• qmule - collection of helper modes for NGS
• qpileup - gathers base-level metrics across a whole genome from a group of BAMs
• qprofiler - QC assessment of BAM files using summary statistics
• qsignature - sample mixup detection
• qsnp - heuristics-based tumour/normal single nucleotide variant (SNV) caller
• qsv - tumour/normal structural variant (SV) caller