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Welcome to the NucDiff wiki manual! You will find here a detailed description of output files, types of differences and information provided for them in the output files.

Output files

Reference-based coordinate files

• _ref_snps.gff
• _ref_struct.gff
• _ref_blocks.gff
• _ref_additional.gff
• _ref_snps.vcf

Query-based coordinate files

• _query_snps.gff
• _query_struct.gff
• _query_blocks.gff
• _query_additional.gff
• _query_snps.vcf

Result statistics

• _stat.out

Types of differences

Local differences

• Insertion
• Duplication
• Tandem duplication, case 1
• Tandem duplication, case 2
• Inserted gap
• Unaligned beginning
• Unaligned end
• Deletion
• Collapsed repeat
• Collapsed tandem repeat, case 1
• Collapsed tandem repeat, case 2
• Substitution
• Gap

Structural differences

• Relocation
• Relocation with overlap
• Relocation with insertion
• Relocation with inserted gap
• Relocation with insertion and inserted gap
• Translocation
• Translocation with overlap
• Translocation with insertion
• Translocation with inserted gap
• Translocation with insertion and inserted gap
• Inversion
• Reshuffling
• Circular genome start

Global differences

• Unaligned sequence

IGV examples

• Example 1