Commit bb586e12 authored by MARIJON Pierre's avatar MARIJON Pierre

Add summary

parent 1769c4bc
......@@ -2,7 +2,21 @@
KNOT: Knowledge Network Overlap exTraction is a tool for the investigation of fragmented long read assemblies.
Give an assembly and a set of reads to KNOT, it will output an information-rich contig graph in CSVformat that tells you about adjacencies between contigs.
Give an assembly and a set of reads to KNOT, it will output an information-rich contig graph in CSV format that tells you about adjacencies between contigs.
- [Input](#input)
- [Output](#output)
- [Usage](#usage)
- [Installation](#installation)
* [Install with conda](#install-with-conda)
* [Install without conda](#install-without-conda)
- [Update](#how-to-update-an-already-installed-knot)
* [Conda installation](#conda-installation)
* [Non-conda installation](#non-conda-installation)
- [More details](#more-details)
* [Pipeline presentation](#pipeline-presentation)
* [Output description](#output-description)
- [Citation](#citation)
## Input
......@@ -28,6 +42,8 @@ Output format is in CSV format with 8 column:
This output can be used to manually investigate the result of an assembly.
Short paths between contigs are likely true adjacencies. Long paths are likely repeat-induced.
More information about other file generated by knot are avaible in [output description](#output-description)
## Usage
Assume that
......@@ -129,9 +145,10 @@ conda env create -f conda_env.yml
```
pip3 install --upgrade git+https://gitlab.inria.fr/pmarijon/knot.git
```
```
# Description of the pipeline
## More details
### Pipeline presentation
![Globale pipeline](images/pipeline.png)
......@@ -143,7 +160,7 @@ Legend:
- output `#5D2971`
- pipeline internal tool `#FFD300`
# All output description
### Output description
If you run knot with raw reads:
```
......@@ -180,6 +197,6 @@ If you run knot with corrected reads:
└── read2asm.paf # mapping of read on contigs_filterd
```
# Citation
## Citation
Please cite this Github URL for now, manuscript is in submission.
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