Biowulf High Performance Computing at the NIH
ImReP: rapid and accurate profiling of the adaptive immune repertoires from regular RNA-Seq data.

ImReP is a novel computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data. It is able to efficiently extract TCR- and BCR-derived reads from RNA-Seq data. ImReP can also accurately assemble the complementary determining regions 3 (CDR3s), the most variable regions of B and T cell receptors, and determine their antigen specificity.

References:

Documentation
Important Notes

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

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g
[user@cn3316 ~]$ module load imrep
[+] Loading ImReP 0.8  ...
[user@cn3316 ~]$ imrep.py  -h
usage: python2 imrep.py [-h] [--fastq] [--bam] [--chrFormat2] [--hg38]
                        [-a ALLREADS] [--digGold] [-s SPECIES] [-o OVERLAPLEN]
                        [--noOverlapStep] [--extendedOutput] [-c CHAINS]
                        [--noCast] [-f FILTERTHRESHOLD]
                        [--minOverlap1 MINOVERLAP1]
                        [--minOverlap2 MINOVERLAP2] [--misMatch1 MISMATCH1]
                        [--misMatch2 MISMATCH2]
                        reads_file output_clones

optional arguments:
  -h, --help            show this help message and exit

Necessary Inputs:
  reads_file            unmapped reads in .fasta (default) or .fastq (if flag
                        --fastq is set) or .bam (if --bam or --digGold is set)
  output_clones         output file with CDR3 clonotypes

Optional Inputs:
  --fastq               a binary flag used to indicate that the input file
                        with unmapped reads is in fastq format
  --bam                 a binary flag used to indicate that the input file is
                        a BAM file mapped and unmapped reads
...
Advanced Inputs:
  --minOverlap1 MINOVERLAP1
                        minimal overlap between the reads and A) the left part
                        of V gene (before C amino acid) and B) the right part
                        of J gene (after W for IGH and F for all other
                        chains), default is 4
  --minOverlap2 MINOVERLAP2
                        minimal overlap between the reads and A) the right
                        part of V gene (after C amino acid) and B) the left
                        part of J gene (before W for IGH and F for all other
                        chains), default is 1
...
[user@cn3316 ~]$ suffix_tree.py
SIMPLE TEST
leaf: "mississippi$" : "mississippi$"
leaf: "ississippi$" : "ssippi$"
leaf: "issippi$" : "ppi$"
leaf: "ippi$" : "ppi$"
leaf: "i$" : "$"
leaf: "ssissippi$" : "ssippi$"
leaf: "ssippi$" : "ppi$"
leaf: "sissippi$" : "ssippi$"
leaf: "sippi$" : "ppi$"
leaf: "ppi$" : "pi$"
leaf: "pi$" : "i$"
leaf: "$" : "$"
inner: "ssi"
inner: "i"
inner: "si"
inner: "i"
inner: "s"
inner: "p"
inner: ""
done.


GENERALISED TEST
----------------------------------------------------------------------
0 [0:1] x |x|abxa
0 [3:4] x xab|x|a
1 [3:4] x bab|x|ba
----------------------------------------------------------------------
0 [1:4] abx x|abx|a
1 [1:4] abx b|abx|ba
----------------------------------------------------------------------
0 [1:2] a x|a|bxa
1 [1:2] a b|a|bxba
0 [4:5] a xabx|a|
1 [5:6] a babxb|a|
----------------------------------------------------------------------
0 [2:4] bx xa|bx|a
1 [2:4] bx ba|bx|ba
----------------------------------------------------------------------
0 [2:3] b xa|b|xa
1 [2:3] b ba|b|xba
1 [0:1] b |b|abxba
1 [4:5] b babx|b|a
======================================================================
----------------------------------------------------------------------
0 [1:4] abx x|abx|a
1 [1:4] abx b|abx|ba
----------------------------------------------------------------------
0 [2:4] bx xa|bx|a
1 [2:4] bx ba|bx|ba
======================================================================
done.

End the interactive session:
[user@cn3316 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$