Update file README.md

README.md

@@ -173,7 +173,7 @@ sh scripts/script_identification_of_viral_contigs_sub.sh
 ```
 
 ### Production of a vOTU abundance table
-Quality-filtered reads vers mapped against the viral contigs using [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) version 2.2.1. Raw counts were extracted using [samtools](https://github.com/samtools/samtools) version 1.9 and [msamtools](https://github.com/arumugamlab/msamtools) version 1.1.3. All command lines were embedded in the script `mapping_viral_contigs.sh` and require the scripts `presence_dico.py` `function.py` and `data_ab_QLB2.py`. The vOTU abundance table was save as a csv file: `results/Viral_prediction/VIRAL_CONTIGS/MAPPING_BWA-MEM2/presence_counts.csv`. The following command line was used to run the script:
+Quality-filtered reads were mapped against the viral contigs using [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) version 2.2.1. Raw counts were extracted using [samtools](https://github.com/samtools/samtools) version 1.9 and [msamtools](https://github.com/arumugamlab/msamtools) version 1.1.3. All command lines were embedded in the script `mapping_viral_contigs.sh` and require the scripts `presence_dico.py` `function.py` and `data_ab_QLB2.py`. The vOTU abundance table was save as a csv file: `results/Viral_prediction/VIRAL_CONTIGS/MAPPING_BWA-MEM2/presence_counts.csv`. The following command line was used to run the script:
 
 Alignments were filtered to retain contigs for which there is sufficient proof of presence, using msamtools v1.1.3 (Arumugam). Firstly, msamtools filter was used toonly keep those with a minimum length of alignment of 80, minimum sequence identity of alignment of 95, and minimum percent of the query that must be aligned 80 and with --besthit option. Then, msamtools coverage estimates the coverage of each sequence, and the --summary option reports the fraction of sequence covered in percentage. Then alignments with more than 50% of horizontal coverture were kept to construct the final abundance tables using data_ab_QLB2.py from Quentin Lamy--Besnier (INRAE, Jouy-en-Josas)
 This last script return csv file: presence_count.csv corresponding to abundance table of vOTUs in each samples.