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Table 1 List of analysis tools providing pre-processing functions

From: VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data

Tool Category Composition statistics calculation Merging paired-end reads Barcode demultiplexing PCR primer removal Length filtering Quality filtering Homopolymer filtering UMI consensus determination Collapsing duplicate reads
AbStar [16] 1 No Yes Yes No Yes Yes No No No
Decombinator [17] 2 No No Yes No No No No Yes No
Ig-HTS cleaner [18] 3 Yes No Yes Yes Yes Yes No No No
IgRepertoire constructor [19] 1 No Yes Yes No No No No Yes No
ImmunediveRsity [20] 1 No No No No Yes Yes No No No
iMonitor [21] 1 No Yes No No Yes Yes No No No
IMSEQ [22] 1 No Yes Yes No Yes Yes No No No
MIGEC [7] 2 No Yes Yes No No Yes No Yes No
pRESTO [13] 3 No Yes Yes Yes Yes Yes No Yes Yes
RTCR [23] 1 No No Yes No Yes Yes No No No
VDJPipe 3 Yes Yes Yes Yes Yes Yes Yes No Yes
TCRklass [24] 1 No Yes No No Yes Yes No No No
Abmining [25] 3 No Yes Yes No Yes Yes Yes No No
ClonoCalc [26] 1 No Yes Yes No No No No No No