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. 2017 Jan 10;19(4):554–565. doi: 10.1093/bib/bbw138

Table 1.

A comparison of the features of open source programs available for processing of HTS TCR sequencesa

Analysis tool nameb Input format Availability (online/stand-alone) Maximum input size (number of sequences) Filtering/error-correction steps built into analysis pipeline
Sequence read quality Unique identifierc Clusteringd Frequencye
1 IMGT/V-QUEST [17] FASTA Online 50 No No No No
2 IMGT/HighV-QUEST [18] FASTA Online—account log in required 150 000 No No Yes No
3 IgBLAST [19] FASTA Online/stand-alone (command line, C ++) <1000 (online)/none (stand-alone) No No No No
4 Decombinator [20] FASTQ Stand-alone (command line, Python) None Yes (barcode quality) Yes Yes (barcode clustering) No
5 Vidjil [21] FASTA/FASTQ Stand-alone (command line, C ++) None No No Yes Yes
6 MiXCR (+ MiGEC) [22] FASTA/FASTQ Stand-alone (command line, Java) None Yes Yes Yes Yes
7 IMonitor [23] FASTA/FASTQ Stand-alone (command line, Perl, R) None Yes No Yes No
8 IMSEQ [24] FASTA/FASTQ Stand-alone (command line, C ++) None Yes No Yes No
9 LymAnalyzer [25] FASTQ Stand-alone (command line/GUI, Java) None No No Yes No
10 TCRklass [26] FASTQ Standalone (command-line, C ++/Perl) None Yes No No No
11 Recover TCR (RTCR) [27] FASTQ Stand-alone (command line, Python) None Yes Yes Yes No
12 TRIg [28] FASTA Stand-alone (command line, Perl) None No No No No

aPrograms listed do not include tools for single-cell analysis, which are mentioned in text.

bFull link to tool Web page:

cMolecular barcoding.

dCombining clones that are similar (according to a distance threshold).

eRemoval of clones occurring less than a frequency threshold.