Preprocessing methods

The preprocessing methods provided in IMDA use the following open software tools: MIGEC, MiXCR and Bowtie2. You can find more information about third party software and the downloads in the section Third party software.

do_MIGEC and do_MiXCR require *.fastq or *.fastq.gz files as input. Furthermore, MIGEC requires a tab-delimited barcodes.txt file. MiXCR allows the use of other libraries. IMDA has been tested using the imgt.201802-5.sv2 library.

Bowtie2 requires *.fastq or *.fastq.gz files and a library. Libraries can be build using the bowtie2-build command. Further we provide a prepared library included in Download with PhiX genome and various TCR sequences.

For the FACS error correction module a tab-delimited pairs.txt file is required.

Format Description

mixcr_library = “–library D:/Forschungsgruppe/KidTrans/MiXCR/imgt.201802-5/imgt.201802-5.sv2” barcodes.txt and pairs.txt have to be provided in case if MIGEC or the FACS error correction module is used, respectively.


#SampleID Master barcode sequence Slave barcode sequence FASTQ#1 FASTQ#2
1_A_nS_r1 NNNNNNtCAGATtNNNNNNtcttgggg   idx1_R1_001.fastq.gz idx1_R2_001.fastq.gz
1_A_nS_r2 NNNNNNtCAGATtNNNNNNtcttgggg   idx2_R1_001.fastq.gz idx2_R2_001.fastq.gz


#SampleID1 SampleID2
1_A_nS_r1 1_A_nS_r2
1_B_nS_r1 1_B_nS_r2

Read Assignment Visualisation

For an immedeiate overview of the progress of the read counts IMDA provides a sankey diagram (Figure 1) showing the raw read counts, the read counts after read assignment by barcode and the read counts after the UMI assembling within MIGEC.


Figure 1: Read assignment within MIGEC - raw read counts (left), read counts after read assignment by barcode (middle), read counts after UMI assembling (right)