pairtools: a command-line framework to process sequencing data from a Hi-C experimen

Pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. Pairtools perform various operations on Hi-C pairs and occupy the middle position in a typical Hi-C data processing pipeline. Pairtools aim to be an all-in-one tool for processing Hi-C pairs.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

[user@biowulf]$ sinteractive --gres=lscratch:10 --mem=0g -c4
[user@cn0861 ~]$ module load pairtools 
[+] Loading singularity  3.8.5-1  on cn4207
[+] Loading pairtools  0.3.0
[user@biowulf]$ python $PT_TESTS/test_dedup.py 

[user@biowulf]$ python $PT_TESTS/test_filterbycov.py 

[user@biowulf]$ python $PT_TESTS/test_flip.py 

[user@biowulf]$ python $PT_TESTS/test_headerops.py 

[user@biowulf]$ python $PT_TESTS/test_markasdup.py 

[user@biowulf]$ python $PT_TESTS/test_merge.py 

[user@biowulf]$ python $PT_TESTS/test_parse.py 

[user@biowulf]$ python $PT_TESTS/test_select.py 

[user@biowulf]$ python $PT_TESTS/test_sort.py 

[user@biowulf]$ python $PT_TESTS/test_split.py 

[user@biowulf]$ python $PT_TESTS/test_stats.py 
etc.
[user@cn0861 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226