compute ANI values between two sequences using windows cmd.exe The batch file (win_batch_ani.bat) calculates ANI values between genomes for two or more genomes present in an equal number of .fasta files. The script produces resulting ANI values as .txt- and a .tsv files.
1.0
24.08.2023
- Dylan Winterflood
- Pascal Schlaepfer
Laboratory Medicine, University Hospital Basel, 4031 Basel, SWITZERLAND
- usearch11.0.667_win32.exe (http://www.drive5.com/usearch/download.html, Version: usearch11.0.667_win32.exe.gz)
- OAU.jar (https://www.ezbiocloud.net/tools/orthoaniu)
- Copy all .fasta files, between which you want to calculate ANI scores, into a single folder. ANI values will be calculated for each combination of 2 .fasta files in this folder. NOTE: only .fasta file endings allowed.
- Copy this .bat file to the same folder where the .fasta files are stored.
- Modify line 50 with the path to your OAU.jar file.
- Modify line 52 with the path to your usearch executable file.
- Save this bat file and close it.
- Execute your .bat file: The calculation now starts. The calculation can take hours to days, depending on the number of .fasta files. (approx. 13 seconds per file, depending on the computer).
- A folder containing at least two fasta files, each with one genome.
(Files generated in search folder)
- status.txt: Text file that shows whether the calculation has already been completed. It is possible that the program is aborted. In this case, simply re-execute this.bat file. The script will then continue where it left off.
- results.txt: Text file containing all calculations of ANI values. This raw data is then converted into a .tsv file.
- result_for_excel.tsv: A TAB separated file containing ANI values, allowing for easy import into EXCEL.
- please modify the paths on line 50 and 52.
- Versions of both usearch11.0.667_win32.exe and OAU.jar included in this build, but you might need other versions, depending on your computer architecture