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:

• Fan Song, Jie Xu, Jesse Dixon and Feng Yue
  Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. Hi-C Data Analysis. Methods and Protocols (2022). pp 143-161

• pairtools Github page
• pairtools Documentatiom

• Module Name: Funannotate (see the modules page for more information)
• Unusual environment variables set
  • PT_HOME  installation directory
  • PT_BIN    executables directory
  • PT_DATA    sample data directory
  • PT_TESTS    test scripts directory

[user@biowulf]$ sinteractive --gres=lscratch:10 --mem=30g -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 

[user@cn0861 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226