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Rebuttal changes #37

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Jan 11, 2025
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Rebuttal changes #37

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7061328
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sumit-walia Jan 11, 2025
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sumit-walia Jan 11, 2025
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -161,10 +161,10 @@ cd $PANMAN_HOME/workflows
conda activate snakemake
snakemake --use-conda --cores 8 --config RUNTYPE="pangraph/gfa/msa" FASTA="None" SEQ_COUNT="Number of sequences" ASSEM="frag" REF="reference_file" TARGET="target.txt"
```
Here, target.txt contains list of files that contains the fragmented assemblies.
Here, target.txt includes a list of files that contain the fragmented assemblies.

## <a name="function"></a> <i>panmanUtils</i> functionalities
<i>panmanUtils</i> provide various functionalities such as summary, [Raw sequence, MSA, VCF, GFA] extract, sub-netwrok pruning, and many more. Please refer to [wiki](https://turakhia.ucsd.edu/panman/) for detailed information. Here we provide usage syntax and examples for summary and VCF extract.
<i>panmanUtils</i> provide various functionalities such as summary, [Raw sequence, MSA, VCF, GFA] extract, sub-network pruning, and many more. Please refer to [wiki](https://turakhia.ucsd.edu/panman/) for detailed information. Here we provide usage syntax and examples for summary and VCF extract.

#### Summary extract
The summary feature extracts node and tree level statistics of a PanMAN, that contains a summary of its geometric and parsimony information.
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4 changes: 4 additions & 0 deletions docs/images/figure1.svg
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8 changes: 4 additions & 4 deletions docs/index.md
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Expand Up @@ -186,13 +186,13 @@ cd $PANMAN_HOME/workflows
conda activate snakemake
snakemake --use-conda --cores 8 --config RUNTYPE="pangraph/gfa/msa" FASTA="None" SEQ_COUNT="Number of sequences" ASSEM="frag" REF="reference_file" TARGET="target.txt"
```
Here, target.txt contains list of files that contains the fragmented assemblies.
Here, target.txt includes a list of files that contain the fragmented assemblies.

## <b>Exploring utilities in <i>panmanUtils</i></b>

Here, we will learn to use exploit various functionalities provided in <i>panmanUtils</i> software for downstream applications in epidemiological, microbiological, metagenomic, ecological, and evolutionary studies.
Here, we will learn to use various functionalities provided in <i>panmanUtils</i> software for downstream applications in epidemiological, microbiological, metagenomic, ecological, and evolutionary studies.

**Step 0:** The Steps below require panmanUtils and a PanMAN. We provide a pre-built panman (`sars_20.panman`), othewise, refer to [installation guide](#install) to install panmanUtils and [construction](#construction) instructions to build a PanMAN.
**Step 0:** The Steps below require panmanUtils and a PanMAN. We provide a pre-built panman (`sars_20.panman`), otherwise, refer to [installation guide](#install) to install panmanUtils and [construction](#construction) instructions to build a PanMAN.
<!-- ```bash
# Assuming $PANMAN directs to the panman repository directory
cd $PANMAN_HOME
Expand Down Expand Up @@ -293,7 +293,7 @@ cd $PANMAN_HOME/build
```

#### Multiple Sequence Alignment (MSA) extract
Extract MSA of sequences for each PanMAT (with pseduo-root coordinates) in a PanMAN in a FASTA format.
Extract MSA of sequences for each PanMAT (with pseudo-root coordinates) in a PanMAN in a FASTA format.

* Usage syntax
```bash
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2 changes: 1 addition & 1 deletion install/installationUbuntu.sh
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@@ -1,6 +1,6 @@
# Install dependencies

sudo apt install -y git build-essential cmake wget curl zip unzip tar libboost-all-dev pkg-config
sudo apt install -y git build-essential cmake wget curl zip unzip tar libboost-all-dev pkg-config protobuf-compiler


# Build
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