trio_binning

This repository contains programs implementing the trio-binning assembly method published by Koren et al.

Installation

Requirements

• kmc (for the find-unique-kmers script only)
• Python
• gcc

Until I get the chance to make a conda package for this, you'll need to install kmc seperately:

conda create -n trio_binning kmc python
conda activate trio_binning

Then you can download and install this package:

git clone https://github.com/esrice/trio_binning.git
cd trio_binning
pip install .

If you get an error like gcc not found you may be on a cluster where gcc needs to be loaded explicitly. Try module load gcc.

Finding unique k-mers in parental genomes

find-unique-kmers is a script that uses the program kmc to find k-mers that are unique to one of the two haplotypes. Here is an example of its usage to find unique 21-mers in short read files from a hybrid's mother and father using 8 threads:

find-unique-kmers -k 21 -p 8 mother_R1.fastq.gz,mother_R2.fastq.gz \
    father_R1.fastq.gz,father_R2.fastq.gz

After running this command, there will be a plain-text list of 21-mers unique to the maternal genome in hapA_only_kmers.txt and the same for the paternal genome in hapB_only_kmers.txt. The working directory will also contain kmc databases for both the total set of 21-mers for each parent and the unique sets. The numbers of unique k-mers for each haplotype is output to STDERR.

Classifying long reads from offspring for assembly

Once you've got lists of k-mers unique to the maternal and paternal genomes, you can use these to classify reads from the offspring into maternal and paternal haplotypes using the program classify-by-kmers, like so:

classify-by-kmers \
    input_reads.fastq.gz \
    hapA_only_kmers.txt \
    hapB_only_kmers.txt \
    --haplotype-a-prefix classified/maternal \
    --haplotype-b-prefix classified/paternal \
    --unclassified-prefix classified/unclassified

This will leave you with three files in the classified directory: paternal.fastq.gz, maternal.fastq.gz, and unclassified.fastq.gz. The input read format is super flexible — you can give this program reads in fasta or fastq format, gzipped or not gzipped.

Citations

• Rice et al. (2020). "Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle." GigaScience 9(4):giaa029
• Koren et al. (2018). "Complete assembly of parental haplotypes with trio binning." Nature Biotechnology 2018/10/22/online