ComponentalphaLicense: MIT
Standalone multi-platform bisulfite alignment, in the style of Clara Parabricks fq2bam_meth and bwa-meth.
GoliathAlign maps whole-genome bisulfite reads on Linux x86-64 and ARM64, on CPU, NVIDIA CUDA, or AMD HIP. The linear aligner, MojoFq2bamMeth, follows the directional C→T / G→A method used by bwa-meth and by NVIDIA Clara Parabricks fq2bam_meth, and writes a coordinate-sorted BAM plus QC JSON. The same install aligns reads to converted genome graphs and calls methylation from the resulting GAF. Install a checkout with pixi, or unpack the Ubuntu 22.04 host runtime published as release 0.1.0-jammy.
MojoFq2bamMeth converts read 1 C→T and read 2 G→A, maps them with an FM-index on a bwa-meth dual-strand reference (k-mer and BWA-MEM engines are selectable), and writes a duplicate-marked BAM, a BAI, and a Parabricks-shaped QC JSON.
Device selection accepts auto, cpu, nvidia (nvidia:sm_90, CUDA), and amd (amdgpu:gfx942 or METHYLGRAPHER_AMDGPU_ARCH, HIP) through Mojo DeviceContext. Pixi solves linux-64 and linux-aarch64.
Align and MojoGiraffe write GAF for C→T and G→A graphs (vg giraffe, or the Mojo Giraffe mapper). MethylCall, MergeCpG, and ConversionRate consume that GAF.
pixi install provides the Mojo toolchain. Release 0.1.0-jammy is goliath-align-host-linux-amd64-jammy.tar.gz, an Ubuntu 22.04 amd64 tree with bin/methylGrapher and a bundled mojo.
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This utility is standalone. It does not declare a dependency on GoliathApp or GoliathOmics.
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