Hi-C and Pore-C support for verkko is finally integrated within main verkko repo, https://github.com/marbl/verkko.
There are lots of improvements there that makes this repo's version completely outdated! If you want to use our phasing separate from verkko assembler, please contact us
This contains scripts for HiC integration in verkko.
Main script to run is all_wrapper.sh It runs hi-c scaffolding pipeline over the preexisting previous verkko (either hifi+ont or hifi+ont+trio) run.
As a prerequirements you'll need to be installed and in $PATH:
- mashmap
- python3 with networkx package
- samtools
Also, you'll need
- pstools (for fast alignment of hi-c reads to the assembly graph). pstools release on github is too old, so we downloaded binaries here https://pstools.s3.us-east-2.amazonaws.com/pstools_1 (recommendation by pstools' author, shilpagarg/DipAsm#16 )
- verkko assembler (for running consensus on resulting paths and for some auxilary scripts)
$PSTOOLS and $VERKKO environment variables should be set to the locations of corresponding tools.
Usage: ./all_wrapper.sh <previous_verkko_run> <output_folder> <reads_folder>
As alternative, with precomputed alignment you can run ./norealign_wrapper.sh <previous_verkko_run> <output_folder> <reads_folder> <aligned_sorted_bam>
For interface simplicity script expects that all input reads are located in <reads_folder>, with hifi/ont/hic subfolders for each data type. Reads can be in {fastq/fasta}.gz format; hic paired reads should be in separate files with names like smthR1.fastq.gz and smthR2.fastq.gz
Final assembly will be in <output_folder>/final_consensus/assembly.fasta