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:

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


    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

Choose a program:

Calculation of diversity indexes

Choose a program:

Network analysis

Choose a program:

Distance tree

Choose a program:

southgreen IRD INRA