Table 1.
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:
1, 2. http://www.imgt.org
cMolecular barcoding.
dCombining clones that are similar (according to a distance threshold).
eRemoval of clones occurring less than a frequency threshold.