Diploid Assembly (PacBio + StrandSeq)

Workflow

1. Create squashed assembly using PacBio reads and wtdbg assembler.
2. Map StrandSeq reads to collapsed assembly.
3. Use SaaRclust to cluster contigs (assign them to chromosomes).
4. Map PacBio + StrandSeq reads back to clustered assembly.
5. Call heterozygous SNPs for long reads.
6. Construct global chromosome length haplotypes using WhatsHap with PacBio and StrandSeq reads.
7. Haplotag and split PacBio reads.
8. Create two de novo assemblies for each parental homolog.

Installation Remarks

- For step 1 and 2 use conda environment provided with pipeline.
- For step 3 create own conda environment "saarclust" with "r-igraph" and "r-biocmanager" installed.

test