SNiPlay Pipeline V2





What is your input(s)? Chromatograms
FASTA alignment   Staden output   Genalys output
Genotyping: PED format   

Number of files:single   collection  



Optionally, you can also provide information on accessions (headers: "Accession, Feature1, Feature2...")
Maximum 3 groups for each category (to enable comparisons)




SNP/INDEL discovery

Choose a program:

Identifiers of sequence:
   individual_xxx_regionName_xxx
   regionName_xxx_individual_xxx
   regionName_individual_xxx
   individual_regionName_xxx
   regionName_xxx_xxx_individual

Special characters
Character used for heterozygous INDEL: L   N
Character used for missing data: ?   N

Missing data:
Truncate sequences : remove positions having more than % missing data

Generation of a submission file for Illumina VeraCode Technology:
Enter the length of flanking sequences

Polymorphism treatment for genotyping files and subsequent analyses:
      Multiallelic SNP treatment:
            Replace minor allele by a missing data
            Replace minor allele by the major allele
            Replace minor allele by the second most frequent allele
            Discard multiallelic SNP
      INDEL treatment:
            Recode INDEL as bi-allelic SNP
            Discard INDEL


Locate and annotate SNPs on a annotated reference genome

Genome:

    Use BlastN to locate SNP on the genome   =>  Expect threshold:
    Reference sequences correspond to CDS. Instead of Blast, use directly the GFF annotation to annotate SNP
    Reference sequences correspond to mRNA (CDS+UTR). Instead of Blast, use directly the GFF annotation to annotate SNP

    Perform an additional TBlastN search for paralog/homeolog estimate


Functional annotation (Blast against Uniprot)


Reconstruction of haplotypes

Choose a program:


Linkage Disequilibrium analysis

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Calculation of diversity indexes

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Network analysis

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Distance tree

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southgreen IRD INRA