Lineage-Specific-Marker

filter the reads

run filter_by_qscore.sh to filter the reads by qscore and then run filter_by_length.ipynb to filter the sequences by length.

cluster and build the consensus

run run_vsearch.sh, this script will run vsearch clustering algorithm on each fasta file and output three files, .uc file stores the cluster information for each sequence, two .fasta files store the centroid and consensus sequences for each cluster

summarize the cluster information

run write_cluster_to_excel.ipynb, this will summarize of cluster information and generate the .xlsx files. There are three columns for each .xlsx file, which stored the centroid sequence and consensus sequence of each cluster

extract the desired consensus

After summarize the cluster information, it would be able to see the large clusters that contain high percentage of sequencces. Build a txt file which stores the id of selected clusters by ascending order and the different groups of ids should also be stored by the ascending order of files. Then run write_consensus_by_cluster.ipynb to get the consensus for each sample.

geneious analysis

After get the consensus sequences, import them to the geneious software and then reorient the consensus sequences, align them and build the phylogenetic trees

Dependency

for python script

python 3.11.5
Biopython 1.78
pandas 2.1.1

for bash file

NanoFilt 2.8.0
vsearch 2.22.1