gpatch 0.3.8

Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.

GPatch

Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.

Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference.

Dependencies

• Python >= v3.7
• samtools (https://github.com/samtools/samtools)
• biopython (https://biopython.org/)
• pysam (https://github.com/pysam-developers/pysam)
• minimap2 (https://github.com/lh3/minimap2)

We recommend using minimap2 for alignment, using the -a option to generate SAM output.

Installation

We recommend installing with conda, into a new environment:

conda create -n GPatch -c conda-forge -c bioconda Bio pysam minimap2 samtools GPatch

Install with pip:

pip install GPatch

Installation from the github repository is not recommended. However, if you must, follow the steps below:

1. git clone https://github.com/adadiehl/GPatch
2. cd GPatch/
3. python3 -m pip install -e .

Usage

usage: GPatch.py [-h] -q SAM/BAM -r FASTA [-x STR] [-b FILENAME] [-m N]
                 [-w PATH] [-d]

Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Reference chromosomes with no mapped contigs are printed to output unchanged.

Required Arguments

Argument	Description
-q SAM/BAM, --query_bam SAM/BAM	Path to SAM/BAM file containing non-overlapping contig mappings to the reference genome.
-r FASTA, --reference_fasta FASTA	Path to reference genome fasta.

Optional Arguments:

Argument	Description
-h, --help	Show this help message and exit.
-x STR, --prefix STR	Prefix to add to output file names. Default=None
-b FILENAME, --store_final_bam FILENAME	Store the final set of primary contig alignments to the given file name. Default: Do not store the final BAM.
-m N, --min_qual_score N	Minimum mapping quality score to retain an alignment. Default=30
-w PATH, --whitelist PATH	Path to BED file containing whitelist regions: i.e., the inverse of blacklist regions. Supplying this will have the effect of excluding alignments that fall entirely within blacklist regions. Default=None
-d, --drop_missing	Omit unpatched reference chromosome records from the output if no contigs map to them. Default: Unpatched chromosomes are printed to output unchanged.
-t, --no_trim	Do not trim the 5-prime end of contigs whose mappings overlap the previously-placed contig. Default: Overlapping contig sequence will be trimmed at the previous 3-prime contig breakpoint.

Output

GPatch produces three output files:

File	Description
patched.fasta	The final patched genome.
contigs.bed	Location of contigs in the coordinate frame of the patched genome.
patches.bed	Location of patches in the coordinate frame of the reference genome.

Citing GPatch

Please use the following citation if you use this software in your work:

Fast and Accurate Draft Genome Patching with GPatch Adam Diehl, Alan Boyle bioRxiv 2025.05.22.655567; doi: https://doi.org/10.1101/2025.05.22.655567