Improvements

Optimized the performance of individual threads in the CPU thread pool during alignment.

Additional optimizations for GPU performance.

Improved error handling when using --gpuwrite option.

Added support for batch processing multiple input FASTQ files by repeatedly applying the --in-fq or --in-se-fq option.

Added support for batch processing multiple input FASTQ files by passing in the --in-fq-list or --in-se-fq-list option, where the input is a text file containing a list of paired-end or single-end FASTQ files.

Added support for single-cell sequencing mode, which can be enabled using the --soloType Droplet option along with additional necessary options including --soloCBwhitelist, --soloFeatures, --soloStrand, and --soloBarcodeReadLength.

Added support for quantification mode using the --quantMode option.

Added support for RNA options --minimizer-kmer-len and --forward-transcript-strand, which are recommended for use in mapping long RNA-seq data in splice modes.

Added argument --mutect-f1r2-tar-gz in mutectcaller to collect F1R2 counts for FFPE samples.

Added support for producing gzipped VCF files by specifying output file name with .vcf.gz extension.

Added support for producing gzipped VCF files by specifying output file name with .vcf.gz extension.

Added support for producing gzipped VCF files by specifying output file name with .vcf.gz extension.

Added support for producing gzipped VCF files by specifying output file name with .vcf.gz extension.

Added support for haplotype sampling, enabling personalized reference pangenome creation per sample.

Added real-time CPU and host memory usage monitoring via ‑‑monitor‑usage flag.