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MiXCR Analyze (version 3.0.5.0)

amplicon or shotgun data:

5’-end of the library.:

There are two possible values: no-v-primers — no V gene primers (e.g. 5’RACE with template switch oligo or a like), v-primers — V gene single primer / multiple.

3’-end of the library.:

There are three possible values: j-primers — J gene single primer / multiplex, j-c-intron-primers — J-C intron single primer / multiplex, c-primers — C gene single primer / multiplex (e.g. IGHC primers specific to different immunoglobulin isotypes).

Presence of PCR primers and/or adapter sequences:

If sequences of primers used for PCR or adapters are present in sequencing data, it may influence the accuracy of V, J and C gene segments identification and CDR3 mapping.

Type of starting material: RNA or DNA:

Single or Paired-end reads:

Select between paired and single end data

Select sequence dataset:

Specify dataset with single reads

Library selector:

Select between paired and single end data

Species:

Assemble full receptor sequences.:

This option may slow down the computation.

Use germline segments (printed with lowercase letters) for uncovered gene features:

Filter out-of-frame and stop-codons in export:

Dedicated receptor type for analysis:

MiXCR a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data

MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.

MiXCR is free for academic and non-profit use (see License).

This tool runs the MiXCR analyze pipeline. Generally, there two distinct types of library preparation which correspond to the two analyze pipelines:

analyze amplicon for analysis of targeted TCR/IG library amplification (5’RACE, Amplicon, Multiplex, etc).

analyze shotgun for analysis of random fragments (RNA-Seq, Exome-Seq, etc).

MiXCR has builtin libraries for human, mouse and rat. Additional compiled IMGT libraries can be imported into your Galaxy history as datatype: imgt.json from: https://github.com/repseqio/library-imgt/releases

NOTE: The imgt.201822-5.sv4.json.gz release has the rattus genus taxonId:10114 for rat, whereas the mixcr builtin library has the rattus norvegicus species taxId:10116 for rat. If you encounter imgt library loading errors from mixcr, you may have to substitute 10116 for 10114 in the imgt.201822-5.sv4.json.gz file.

Data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)."