Readme.md

Workflows

Workflow diagram

Workflow steps

1 - Generate diploid pseudomolecules with HaploSplit.

2 - Pseudomolecule quality control.

3 - Manipulate genomic sequences with HaploBreak and HaploMake.

4 - Improve pseudomolecules by filling gaps.

5 - Phase haplotypes.

Workflows

Draft to phased pseudomolecules

1. Perform input QC and generate a first set of pseudomolecules using HaploSplit (1 - Generate diploid pseudomolecules with HaploSplit)
   • 1.a: If input sequences need editing, you may want to correct them first (3 - Manipulate genomic sequences with HaploBreak and HaploMake), then return to step 1 to produce corrected pseudomolecules.
2. Perform a QC of the assembly results with HaploDup (2 - Pseudomolecules quality control.). According to the results, you may need to:
   • 2.a: correct the input sequences (3 - Manipulate genomic sequences with HaploBreak and HaploMake) and perform step 1 again (1 - Generate diploid pseudomolecules with HaploSplit) .
   • 2.b: update the constraints between sequences using previously unknown haplotype-to-haplotype relationships and perform step 1 again (1 - Generate diploid pseudomolecules with HaploSplit) .
3. Improve the assembly information by filling gaps with HaploFill (4 - Improve pseudomolecules by filling gaps.)
4. Perform a QC of the assembly results with HaploDup (2 - Pseudomolecules quality control). According to the results, the procedure may require the following:
   • 4.a: if errors are present in the scaffolds, correct the input sequences (3 - Manipulate genomic sequences with HaploBreak and HaploMake), then return to Step 1 to produce corrected pseudomolecules.
   • 4.b: update the constraints between sequences using previously unknown haplotype-to-haplotype relationships and perform step 1 again (1 - Generate diploid pseudomolecules with HaploSplit) .
   • 4.c: further improve the assembly by re-iterating step 3, HaploFill (4 - Improve pseudomolecules by filling gaps.)
   • 4.d: if the the results are satisfactory, process the results with HaploMap to extract the phasing information map (5 - Phase haplotypes).

Pseudomolecule QC and improvement

1. Perform a QC of the assembly results with HaploDup (2 - Pseudomolecules quality control.). According to the results, you may need to:

   • Correct the sequences:
     1. correct the input sequences (3 - Manipulate genomic sequences with HaploBreak and HaploMake)
     2. perform HaploSplit (1 - Generate diploid pseudomolecules with HaploSplit)
     3. return to step 1 and perform a QC of the assembly results with HaploDup (2 - Pseudomolecules quality control.).
   • Improve the assembly information:
     1. Fill gaps with HaploFill (4 - Improve pseudomolecules by filling gaps.)

2. Perform a QC of the assembly results with HaploDup (2 - Pseudomolecules quality control). According to the results, the procedure may require the following:

   • if errors are present in the scaffolds, correct the input sequences (3 - Manipulate genomic sequences with HaploBreak and HaploMake), then return to Step 1 to produce corrected pseudomolecules.
   • update the constraints between sequences using previously unknown haplotype-to-haplotype relationships and perform step 1 again (1 - Generate diploid pseudomolecules with HaploSplit) .
   • further improve the assembly by re-iterating step 3, HaploFill (4 - Improve pseudomolecules by filling gaps.)

3. If the the results are satisfactory, process the results with HaploMap to extract the phasing information map (5 - Phase haplotypes).