REPcluster aim to cluster repeat sequences that have similar contents but distinct structures, such as (TTTAGGG)m vs (TTTAGGG)n (tandem repeats), A-B-C vs A-C (some TE sequences).
Quick install and start
git clone https://github.com/zhangrengang/REPcluster
cd REPcluster
# install
conda -c bioconda kmer-db mcl xopen
python3 setup.py install
# run an example
cd example_data
REPclust hifi.trf.fa -x 2 # for tandem repeats
Outputs
repclust.a2a.csv.jaccard # Similariry matrix
repclust.network # Network to import into Cytoscape
repclust.attr # Attibutes to import into Cytoscape
repclust.mcl # one Cluster per line
repclust.fa # centered sequences for each cluster
Usage
usage: REPclust [-h] [-pre STR] [-o DIR] [-tmpdir DIR] [-x INT] [-k INT]
[-m {jaccard,min,max,cosine}] [-c FLOAT] [-I FLOAT] [-p INT]
[-cleanup] [-overwrite] [-v]
FILE [FILE ...]
Cluster Repeat Sequences.
optional arguments:
-h, --help show this help message and exit
Input:
FILE Each sequence in a FASTA file is treated as a separate
sample
Output:
-pre STR, -prefix STR
Prefix for output [default=repclust]
-o DIR, -outdir DIR Output directory [default=.]
-tmpdir DIR Temporary directory [default=tmp]
Kmer matrix:
-x INT, -multiple INT
Repeat sequences to cluster tandem repeat or circular
sequences [default=1]
-k INT Length of kmer [default=15]
-m {jaccard,min,max,cosine}, -measure {jaccard,min,max,cosine}
The similarity measure to be calculated.
[default=jaccard]
Cluster:
-c FLOAT, -min_similarity FLOAT
Minimum similarity to cluster [default=0.2]
-I FLOAT, -inflation FLOAT
Inflation for MCL (varying this parameter affects
granularity) [default=2.0]
Other options:
-p INT, -ncpu INT Maximum number of processors to use [default=32]
-cleanup Remove the temporary directory [default=False]
-overwrite Overwrite even if check point files existed
[default=False]
-v, -version show program's version number and exit