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.

vlad0x00/physlr