# 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. |
## 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:
CITATION_HERE
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