<commit_before># GEAN (Version: Beta)

The gene sequence and genetic feature variation between different individuals are very important for natural variation research. And the genome sequence and genetic features (always in GFF/GTF format) of reference is well established. In general the genomic sequence of different lines/accession are sequenced.
The genetic features of variant individuals are also very interesting, while there no well established solution to transform the genetic features annotation of reference accession/line to other individuls. This pipeline tries transform the reference genetic fearures to variant individuls with genome sequence avaliable by whole-genome resequencing or *de novo* assembly . Here we provide a solution for [inconsistent alignment problem](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007699) which could lead to false positive splice sites disturb or ORF-shift predication. And whole genome MSA is all developped basing on the genetic features.
GEAN could also use to transform the well annotated genetics feature of model species to phylogenetically nearby species with whole genome newly sequenced .

<p align="center">
<img src="./doc/alternativeAlignment.gif" width="450px" background-color="#ffffff" />
</p>
Here GEAN solved this problem by a dynamic programming algorithm (Zebric stripped dynamic programming).
This pipeline could help to peform analysis where the gene structure annotaion of different accessions might important such the natural variation of certain single interesting gene, quantify the gene expression for non-reference accession/line and detect the difference expression level across different accession/line. 

Using the gene annotation as anchors, GEAN could perform base-pair resolution whole-genome-wide sequence alignment and perform variant calling.

## Install
### Dependencies
CPU support avx2\
GCC >=6.0 \
Cmake >- 3.0
```<commit_msg>typo fix<commit_after># GEAN (Version: Beta)

The gene sequence and genetic feature variation between different individuals are very important for natural variation research. And the genome sequence and genetic features (always in GFF/GTF format) of reference is well established. In general the genomic sequence of different lines/accession are sequenced.
The genetic features of variant individuals are also very interesting, while there no well established solution to transform the genetic features annotation of reference accession/line to other individuls. This pipeline tries transform the reference genetic fearures to variant individuls with genome sequence avaliable by whole-genome resequencing or *de novo* assembly . Here we provide a solution for [inconsistent alignment problem](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007699) which could lead to false positive splice sites disturb or ORF-shift predication. And whole genome MSA is all developped basing on the genetic features.
GEAN could also use to transform the well annotated genetics feature of model species to phylogenetically nearby species with whole genome newly sequenced .

<p align="center">
<img src="./doc/alternativeAlignment.gif" width="450px" background-color="#ffffff" />
</p>
Here GEAN solved this problem by a dynamic programming algorithm (Zebric stripped dynamic programming).
This pipeline could help to peform analysis where the gene structure annotaion of different accessions might important such the natural variation of certain single interesting gene, quantify the gene expression for non-reference accession/line and detect the difference expression level across different accession/line. 

Using the gene annotation as anchors, GEAN could perform base-pair resolution whole-genome-wide sequence alignment and perform variant calling.

## Install
### Dependencies
CPU support avx2\
GCC >=6.0 \
Cmake >= 3.0
```
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