dreammaerd/pacbio-tools repository overview

dreammaerd/pacbio-tools:v2 is a Docker image for calling SV with PacBio sequencing data. This image is built on top of the Micromamba-based Mambaforge distribution. It includes tools pbmm2, pbsv, and pbtk, alongside samtools, bcftools, and htslib (which includes bgzip and tabix).

⁠Key Features

⁠PacBio Tools:

• pbmm2: Align PacBio reads with optimized performance for long-read data.
• pbsv: Discover and genotype structural variants in PacBio data.
• pbtk: Perform a variety of toolkit operations on PacBio data.

⁠General Sequence Handling:

• samtools: Perform a range of operations on SAM, BAM, and CRAM files.
• bcftools: Manipulate and analyze variant call format (VCF) and binary variant call format (BCF) files.
• htslib: Provides bgzip for file compression and tabix for indexing, crucial for working with large genomic datasets.

⁠Base Image

Built on mambaorg/micromamba:1.2.0, leveraging Micromamba for efficient package management and a minimal footprint.