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

BMC Bioinformatics

Table 1 List of analysis tools providing pre-processing functions

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

ISSN: 1471-2105