Method | Description | Input (I)/Output (O) |
---|---|---|
MIGEC | Read assignment by barcode (de-multiplexing) and consensus assembling based on UMIs using the open-source tool MIGEC. | I: NGS files in compressed or non-compressed FASTQ file format O: assembled reads in FASTQ file format |
MiXCR | Execution of MiXCR commands for clonotype identification and quantification for receiving nucleotide and AA sequences of the CDR3 region and V(D)J gene segments. | I: files in compressed or non-compressed FASTQ file format O: immune repertoire profiling measures (e.g., V(D)J gene segments, CDRs etc.) in text file format |
ContaminationAnalysis | Calculates shared UMIs and V(D)J hits of multiple samples for cross-sample contamination analysis. | I: MiXCR output, MIGEC output or non-compressed FASTQ files containing the UMI sequence in the read ID O: cleaned FASTQ files |
FACSCorrection | Cell subset disambiguation of clonotypes from cells separated using FACS or magnetic sorting (e.g., CD4+ and CD8+) and elimination of clonotypes within a twofold change range. | I: filename of pairs for analysis (pairs.txt) and MiXCR output O: cleaned files in MiXCR text file format |
VDJtools | Executes methods of the open-source tool VDJtools (convert and calculate diversity indices) for diversity stats visualization later-on. | I: MiXCR output O: diversity indices for all samples |
Bowtie | Analyze undetermined reads from sequencing run and from MIGEC assignment using the open-source tool Bowtie2 for non-assignable read composition analysis. | I: file path to the undetermined files in compressed or non-compressed FASTQ file format and to MIGEC undef-m output file, and path to Bowtie2 library O: mapping information is collected in SAM file format |
EvaluateUndetermined | If undetermined read analysis using Bowtie2 has been performed, evaluation and visualization of the results is done. | I: the Bowtie2 output in SAM file format O: read counts for each category (see Undetermined Read Processing and Analysis) |
ClonalityAnalysis | Clonotype and CDR3 sequence length analysis and visualization is performed. | I: MiXCR output O: CDR3 AA length distribution and clonotype counts |
DiversityAnalysis | Diversity curves are calculated and visualized as well as the diversity indices calculated using VDJtools. | I: MiXCR output and VDJtools output O: diversity curves and diversity measures |
OverlapAnalysis | Shared clonotype analysis and visualization. | I: MiXCR output O: shared clonotype overlaps (heatmap and LM plots) |
SimilarityAnalysis | Hierarchical clustering of all samples is performed and visualized. | I: MiXCR output O: hierarchical clustering information |
VDJAnalysis | Calculation of V and J gene segment pairings and visualization using Chord diagrams. | I: MiXCR output O: chord diagrams |