GEAN · [![license][license-badge]][license]

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 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
GNU GCC >=6.0
Cmake >= 3.0

git clone https://github.com/baoxingsong/GEAN.git
cd GEAN
cmake CMakeLists.txt
make

this command will generate an executable file named gean

<!-- ## Run it ```` Program gean Usage: gean <command> [options] Commands: -- variant calling: pseudogeno create pseudo genome sequence lift transform coordinate to another accession revlift transform coordinate of another accession to reference liftgff transform all the GFF/GTF coordinates revliftgff transform all the GFF/GTF coordinates back to reference reanva update variants records for functional annotation gff2seq get the protein/CDS/gene sequence of GFF/GTF file annowgr annotate re-sequenced genome randomVar assign a random position for each variant -- whole genome wide MSA: premsa cut the whole genome sequence into fragments msatosdi generate sdi files from MSA results -- de novo assembly genome: transgff trans reference gff/gtf to de novo assembly genome purifygff purify the result from transgff ```` #### pseudogeno Get pseudo-genome sequence of re-sequencing accession/line using reference genome sequence and variant calling records. ```` Usage: gean pseudogeno -r reference -v variants -o output Options -h produce help message -r FILE reference genome in fasta format -v FILE variant calling result in vcf/sdi format -p STRING prefix for vcf records -o FILE output pseudo genome in fasta format ```` ** -prefix is the prefix of chromosome name for vcf/sdi variant records. Like the chromosome in TAIR10 reference genome is Chr1, Chr2, Chr3, Chr4 and Chr5. While the chromosomes in vcf files from the 1001 genomes project were indicated with 1, 2, 3, 4 and 5. So `-prefix Chr` should be set to make the software work properly. If this parameter is not set correctly, the software would act as no variant records in the input vcf/sdi file. #### lift Project/liftover a certain reference genome-sequence coordinate to re-sequencing accession/line pseudo-genome-sequence. ```` Usage: gean lift -v variants -c chromosome -p position Options -h produce help message -r FILE reference genome in fasta format -v FILE variant calling result in vcf/sdi format -f STRING prefix for vcf records -c STRING chromosome -p INT the position/coordinate in reference genome ```` #### revlift Project/liftover a certain coordinate of re-sequencing accession/line pseudo-genome-sequence to reference genome-sequence. ```` Usage: gean revlift -v variants -c chromosome -p position Options -h produce help message -r FILE reference genome in fasta format -v FILE variant calling result in vcf/sdi format -f STRING prefix for vcf records -c STRING chromosome, should be consistent with the chromosome information in sdi file (The coordinate starts from 1) -p INT the position/coordinate in re-sequenced genome ```` #### liftgff Inference the gene structure (gtf/gff file) annotation of re-sequencing accession/line by purely coordinate liftover. ```` Usage: gean liftgff -v variants -i inputGffFile -o outputGffFile Options -h produce help message -r FILE reference genome in fasta format -v FILE variant calling result in vcf/sdi format -i FILE the input GFF/GTF file of reference line/accession -f STRING prefix for vcf records -o the output GFF/GTF file of target line/accession ```` #### revliftgff Project/liftover the gene structure (gtf/gff file) annotation of re-sequencing accession/line to reference genome-sequence by purely coordinate liftover. ```` Usage: gean revliftgff -v variants -i inputGffFile -o outputGffFile Options -h produce help message -r FILE reference genome in fasta format -v FILE variant calling result in vcf/sdi format -i FILE the input GFF/GTF file of non-reference line/accession -f STRING prefix for vcf records -o the output GFF/GTF file of reference line/accession ```` #### reanva Realign the sequence using ZDP algorithm to solve the inconsistent INDEL alignment problem and recall all variants which could cause false positive ORF-state shit predication. ```` Usage: gean reanva -i inputGffFile -r inputGenome -a similar segments -s new genome sequence -o output GFF/GTF file Options -h produce help message -i FILE GFF/GTF file -r FILE reference genome sequence -v FILE variant calling result in vcf/sdi format -f STRING prefix for vcf records -o FILE output file -m INT minimum intron size ```` * By ORF-states, this software has following criteria: 1) Splicing sites is one of motif in "SpliceSites", which is included in the release 2) The minimum length of intron is larger than a certain value 3) CDS sequence length is larger than a certain value 4) The length of CDS sequence is divisible by 3 5) No premature stop codon 6) End with end codon 7) Start with start codon The IUPAC Codes of DNA sequence could be well dealt with. The result of ORF-states are included in the CDS sequence #### gff2seq Extract CDS sequence, C-DNA sequence and protein sequence for each protein-coding transcript. And predict the protein coding potential (termed as ORF-state) ```` Usage: gean gff2seq -i inputGffFile -r inputGenome -p outputProteinSequences -c outputCdsSequences -g outputGenomeSequences Options -h produce help message -i FILE reference genome in GFF/GTF format -r FILE genome sequence in fasta format -m INT minimum intron size for ORF stats checking -p FILE output file of protein sequence in fasta format -c FILE output file of CDS (without intron) in fasta format -g FILE output file of transcript (with intron) in fasta frormat ```` #### annowgr Transform the reference gene structure annotation to re-sequencing accession/lines with several complementary methods. ```` Usage: gean annowgr -i inputGffFile -r referenceGenomeSequence -v variants -o outputGffFile Options -h produce help message -i FILE reference GFF/GTF file -n FILE the de novo annotation GFF of the target accession -r FILE reference genome in fasta format -v FILE variant calling result in vcf/sdi format -o FILE the output GFF/GTF file -m INT minimum intron size -d remove reference ORF shift transcripts (default false) -f STRING prefix for vcf records -t INT number of threads, default: 4 -l INT longest transcript to align. default(50000) ```` #### randomVar Assign a random position for each variant in a variant calling result file, which could be used to compare the different between observed variant calling and random variants. ```` Usage: gean generateRandomSdi -v variants Options -h produce help message -r (string) reference genome in fasta format -v variant calling result in vcf/sdi format -o prefix of output file ```` ### Whole genome wide multiple sequence alignment pipeline (under testing) #### premsa cut the genome sequence of a population of individuals into fragments to perform multiple sequence alignment for each fragment. ```` Usage: gean premsa -i inputGffFile -r referenceGenomeSequence -v variants Options -h produce help message -i FILE the input GFF/GTF file of reference line/accession -r FILE reference genome -v FILE list of variant calling results files -f STRING prefix for vcf records -m INT minimum intron size -t INT number of threads, default: 4 -w INT window size, default: 10000 -s INT window overlap size, default: 500 -p INT output catch size (default 100) -l INT longest transcript to align. default(50000) ```` #### msatosdi perform variant calling from the multiple sequence alignment of sequence fragments of a population of genome sequences ```` Usage: gean msatosdi -i inputGffFile -r referenceGenomeSequence -v variants -o outputGffFile Options -h produce help message -a FILE accession list -c FILE chromosome list -