Commit 7a097515 authored by MARIJON Pierre's avatar MARIJON Pierre

Improved presentation of the demo data set

parent 9a30d695
......@@ -18,6 +18,8 @@ Give an assembly and a set of reads to KNOT, it will output an information-rich
* [Output description](#output-description)
- [Citation](#citation)
You can find a demo dataset and instructions for using it, in the demo folder of this repository.
## Input
1) long reads (corrected or not) FASTA (no FASTQ allowed)
......
......@@ -2,7 +2,7 @@
This is a 20x synthetic dataset created by LongISLND, with pacbio error model, on *Terriglobus roseus* (NC_108014.1).
Assembled with canu 1.7.1 `genomeSize=5m --corOutCoverage=20`.
Assembled with canu 1.7.1 with parameter `genomeSize=5m --corOutCoverage=20`.
# File description
......@@ -13,14 +13,16 @@ Assembled with canu 1.7.1 `genomeSize=5m --corOutCoverage=20`.
# How to run knot
We assume knot is avaible in your path and you are in demo folder.
On raw read:
```
knot -r demo/reads_raw.fasta -c demo/assembly_contig.fasta -g demo/assembly_graph.gfa -o raw
knot -r reads_raw.fasta -c assembly_contig.fasta -g assembly_graph.gfa -o raw
```
On corrected read:
```
knot -C demo/reads_raw.fasta -c demo/assembly_contig.fasta -g demo/assembly_graph.gfa -o raw
knot -C reads_raw.fasta -c assembly_contig.fasta -g assembly_graph.gfa -o corrected
```
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