Physlr: Construct a Physical Map from Linked Reads

Physlr constructs a de novo physical map using linked reads from 10X Genomics or stLFR. This physical map can then be used to scaffold an existing assembly to yield chromosomal level contiguity.

Dependencies

• ntCard
• ntHits
• GCC 5 or newer with OpenMP and boost
• Python 3.5 or newer and the following packages
  • community
  • networkx
  • numpy
  • scipy
  • sklearn
  • tqdm

Additionally, we recommend using pypy3 over regular python3 for speed.

Optional dependencies

• pigz for parallel gzip
• zsh for reporting time and memory usage

Compiling Physlr from source

pip3 install --user git+https://github.com/bcgsc/physlr
git clone https://github.com/bcgsc/physlr
cd physlr/src && make install

To install Physlr in a specified directory:

pip3 install --user git+https://github.com/bcgsc/physlr
git clone https://github.com/bcgsc/physlr
cd physlr/src && make install PREFIX=/opt/physlr

Running Physlr

Generating Physlr Physical Map with stLFR reads

To construct a physical map, you need linked reads from 10X Genomics or stLFR. In addition, to visualize the correctness and contiguity of the physical map, you need a reference genome. In this example, the linked reads and reference genome are called linkedreads.fq.gz and reference.fa, respectively. The linked reads are from stLFR so we specify minimizer_overlap=stLFR to use the default value for stLFR reads.

cd experiment
bin/physlr-make physical-map lr=linkedreads ref=ref minimizer_overlap=stLFR

Scaffolding a draft assembly with Physlr Physical Map

To scaffold a draft assembly, you need linked reads from 10X Genomics or stLFR, and an existing assembly. In addition, to calculate Quast summary metrics for the Physlr scaffolded assembly, you need a reference genome. In this example, the linked reads, draft assembly, and reference genome are called linkedreads.fq.gz, draft.fa, reference.fa, respectively. The linked reads are from 10X Genomics so we specify minimizer_overlap=10X to use the default value for 10X Genomics reads.

cd experiment
bin/physlr-make scaffolds lr=linkedreads ref=reference draft=draft minimizer_overlap=10X

See the help page for further information. bin/physlr-make help

Output files

• lr.physlr.physical-map.path: Paths of barcodes (backbones).
• lr.physlr.physical-map.ref.n10.paf.gz.*.pdf: Various graphs showing the contiguity and correctness of the backbones with respect to the reference.
• draft.physlr.fa: Physlr scaffolded assembly using the physical map.
• draft.physlr.quast.tsv: Quast metrics comparing the Physlr scaffolded assembly against the reference.

Acknowledgements

This projects uses:

• btl_bloomfilter BTL C/C++ Common bloom filters for bioinformatics projects implemented by Justin Chu
• nthash rolling hash implementation by Hamid Mohamadi
• readfq Fast multi-line FASTA/Q reader API implemented by Heng Li
• robin-map C++ implementation of a fast hash map and hash set using robin hood hashing by Thibaut G.