#scAllele

scAllele is a versatile tool to detect and analyze nucleotide variants in scRNA-seq. \

scAllele makes use local reassembly via de-Bruijn graph to identify sequence differences and 
infers nucleotide variants at the read level. \

The read level variant-call allows for the analysis of the role variants in the contect of splicing. \
Using mutual information, scAllele identifis allelic linkage between nucleotide variants and splicing 
isoforms. 

Please visit https://github.com/gxiaolab/scAllele for more details. \


## Download (PyPi)

scAllele is available through PyPi. To download simply type: 

```
$ pip install -i https://test.pypi.org/simple/ scAllele
```

If succesful, the program is ready to use. The intallation incorporates console scripts entrypoints to directly 
call scAllele: 

```
$ scAllele
>> [DATE, TIME]	MEM	COMMAND = '/path/to/home/bin/scAllele'
>> A variant caller and variant analysis for scRNA-seq data
>> Usage: 
>>	scAllele -b <file.bam> -g <genome.fa> -o <output prefix>
```

You can also view all the options by typing:

```
scAllele --help
```

## Source code 

If you downloaded the source code (python scripts) then you can directly call scAllele

```
python /path/to/src/scAllele.py -b <file.bam> -g <genome.fa> -o <output prefix> 
```

Make sure scAlele libraries ('gqv' python scripts and 'glm' folder) are in the same directory as scAllele.