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Physlr `physical-map` constructs a *de novo* physical map using linked reads from 10X Genomics or MGI stLFR. This physical map can then be used for various genomics analyses, including scaffolding. Physlr `scaffolds` uses the physical map generated in the first stage to scaffold an existing genome assembly to yield chromosome-level contiguity.
You can install Physlr either via Conda or by compiling from source. We recommend installing Physlr via [Conda](https://docs.conda.io/en/latest/) package manager (Linux, MacOS), which will handle compilation and dependencies automatically.
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## Install Physlr using Conda
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In an active `conda` environment:
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```
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conda install -c bioconda physlr
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physlr help
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```
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Physlr can generate complmentary reports (included in the pipeline by default) - you can install dependencies for these optional features using conda:
Physlr constructs a *de novo* physical map using linked reads from 10X Genomics or MGI stLFR. This physical map can then be used to scaffold an existing assembly to yield chromosome-level contiguity.
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or, to install Physlr in a specified directory (like `/opt/physlr`):
To construct a physical map _de novo_, you need linked reads (from 10X Genomics or MGI stLFR).
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In this example, the linked reads dataset is called `linkedreads.fq.gz`. The linked reads are from stLFR so we specify `protocol=stlfr` to use the default value for stLFR reads.
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```
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cd experiment # Change to working directory
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bin/physlr-make physical-map lr=linkedreads protocol=stlfr # Constructs the physical map
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physlr physical-map lr=linkedreads protocol=stlfr # Constructs the physical map
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```
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You also have the option to provide a reference genome (with `ref`) for Physlr to evaluate the physical map. Assuming the reference is called `reference.fa`, you can run the following command for the previous example:
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```
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cd experiment
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bin/physlr-make physical-map lr=linkedreads ref=reference protocol=stlfr # Constructs the physical map and reference-based evaluations for it
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physlr physical-map lr=linkedreads ref=reference protocol=stlfr # Constructs the physical map and reference-based evaluations for it
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```
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If you provide a reference genome, Physlr first constructs a physical map and then maps it to the input reference. In this case, Physlr automatically outputs a `*.map-quality.tsv` file reporting assembly-like quality metrics for the physical map. In addition, Physlr visualizes the correctness and contiguity of the physical map.
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You can also independently run the physical map construction and evaluation steps:
## Scaffolding a draft assembly with Physlr Physical Map
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## Scaffold an assembly
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To scaffold a draft assembly, you need linked reads from 10X Genomics or stLFR, and an existing assembly.
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In this example, the linked reads and draft assembly are called `linkedreads.fq.gz` and `draft.fa`, respectively. The linked reads are from 10X Genomics so we specify `protocol=10x` to use the default value for 10X Genomics reads.
@echo "To ensure that the pipeline runs correctly, make sure that the following tools are in your PATH: ntCard, ntHits, and Quast."
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@echo "To ensure that the pipeline runs correctly, make sure that the following tools are in your PATH: ntCard (ntcard), ntHits (nthits), and QUAST (quast)."
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