Galaxy | CropGalaxy | Published Workflow | Genomic Selection workflow2.3 - Diversity, statistics and population structure (SNiPlay)

Published Workflows | dereeper | Genomic Selection workflow2.3 - Diversity, statistics and population structure (SNiPlay)

Galaxy Workflow ' Genomic Selection workflow2.3 - Diversity, statistics and population structure (SNiPlay)'

Step	Annotation
Step 1: Input dataset Input hapmap select at runtime
Step 2: Convert genotyping data Input genotyping file Output dataset 'output' from step 1 Format for output file VCF Keep metadata True
Step 3: VCFtools Filter VCF input Output dataset 'output' from step 2 Output file basename filtered Samples Unavailable. Chromosomes Unavailable. Output format VCF Minimum MAF. 0.001 Maximum MAF. 0.5 Missing data proportion 0.0 Minimum number of alleles 2 Maximum number of alleles 2 Polymorphisms All Lower bound 1 Upper bound 100000000
Step 4: VCFtools Filter VCF input Output dataset 'fileout' from step 3 Output file basename filtered Samples Unavailable. Chromosomes Unavailable. Output format plink Minimum MAF. 0.001 Maximum MAF. 0.5 Missing data proportion 0.0 Minimum number of alleles 2 Maximum number of alleles 2 Polymorphisms SNP Lower bound 1 Upper bound 100000000
Step 5: VCFtools Stats VCF input Output dataset 'fileout' from step 3 Output file basename vcf_stats
Step 6: VCFtools SlidingWindow VCF input Output dataset 'fileout' from step 3 Output file basename snp_density Window size (in bp) 200000 (optionnal) Groups select at runtime
Step 7: SNP density VCF input Output dataset 'fileout' from step 3 Step 200000 Output name densities
Step 8: sNMF VCF file Output dataset 'fileout' from step 3 K min 2 K max 5 Minimum admixture proportion percentage for group assignation 50
Step 9: Ped2Fasta PED input Output dataset 'fileout' from step 4 Output file name filtered
Step 10: Cut Cut columns c1,c2,c3 Delimited by Tab From Output dataset 'fileout_snp' from step 6
Step 11: Cut Cut columns c1,c2,c4 Delimited by Tab From Output dataset 'fileout_tstv' from step 6
Step 12: PLINK: MDS plot VCF input Output dataset 'fileout' from step 3 Groups Output dataset 'best_k_groups' from step 8 Output name analyse
Step 13: Readseq Fasta alignment input Output dataset 'fileout' from step 9 Output name phylip conversion Output format 12.Phylip\|Phylip4
Step 14: CircosJS Values for Chromosome Length select at runtime tracks track 1 Track name SNP density Track type Line Track data Output dataset 'out_file1' from step 10 track 2 Track name TsTv Track type Line Track data Output dataset 'out_file1' from step 11
Step 15: FastME Fastme input Output dataset 'fileout' from step 13 Output name Newick tree Data type DNA Evolutionary model F84 Equilibrium frequencies False Gamma distributed rates across sites No Remove gap strategy Pairwise deletion of gaps Distance algorithm BIONJ Tree Refinement BalME SPR Bootstrap No
Step 16: Rooting Newick tree input Output dataset 'outputTree' from step 15 Output name out tree
Step 17: InTreeGreat Newick input Output dataset 'fileout' from step 16 Groups for colorization Output dataset 'best_k_groups' from step 8

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dereeper

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