ARBitR

ARBitR performs overlap-aware scaffolding of draft genome assemblies by using 10X Chromium linked reads (BX tag) from position-sorted BAM/SAM alignments to detect contig overlaps and improve assembly contiguity.

Key Features:

• Overlap-Aware Scaffolding: Implements an overlap-layout-consensus (OLC) approach to detect and resolve overlaps between contigs instead of inserting arbitrary gaps.
• 10X Chromium Integration: Uses position-sorted BAM/SAM read alignments containing 10X Chromium barcodes in the BX tag to inform linking of contigs.
• Contig Sorting and Merging: When provided with a reference genome FASTA used for mapping, can sort and merge contigs into scaffolds to improve continuity.
• Implementation: Implemented in Python3 and intended to run on Unix-based systems.

Scientific Applications:

• Genome Assembly Improvement: Enhances draft genome assemblies by resolving overlaps and reducing artificial gap insertion to produce more contiguous sequences.
• Genomics Research: Supports comparative genomics, evolutionary studies, and functional genomics by providing more accurate scaffolds for downstream analyses.

Methodology:

Integrates linked read information from position-sorted BAM/SAM alignments with BX tags and applies an overlap-layout-consensus (OLC) strategy to detect and resolve overlaps between contigs; can sort and merge contigs using a reference FASTA used for mapping.