MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
With this release we continue extending the set of supported single-cell protocols by adding new ready-to-use presets to our collection. Additionally to newly supported protocols and features required for their reliable processing this release comes with many usability optimizations and stability improvements. See details below:
exom-cdr3
and exom-full-length
-allAAFeatures <from_reference_point> <to_reference_point>
)-uniqueTagsCount
- -allUniqueTagsCount
; allows to export counts of unique tag combinations (useful for protocols with multiple CELL
and UMI
barcodes)findAlleles
commandassemble
; increases productive consensus count for cases with multi-variant tag groups (i.e. birthday paradoxes in UMI data or single-cell data analysis without UMIs)--use-local-temp
, --threads
, --not-aligned-R1
(R2
) and --not-parsed-R1
(R2
) are now available in analyze
, additionally to individual step commandsMiXCR 4.1 features two major functional upgrades:
Along with these features, release brings radically simplified user interface, which reduces all the complexities of repertoire analysis pipeline down to a single command, where only one option, the “preset”, has to be specified. MiXCR 4.1 is shipped with many of specifically optimized presets, for most of the repertoire analysis cases. Upgrades, introduced in this release, also significantly increases transparency of analysis pipeline, by providing a diverse set of new graphical QC reports and adding dozens of new metrics to textual and JSON reports. Additionally, this release incorporates tens of important fixes, performance optimizations and stability improvements.
Along with the software release, we present a new documentation portal. It features a clean content organization, informative illustrations, deep guides on many real-world repertoire analysis scenarios and detailed descriptions for each of the MiXCR commands and analysis presets.
Welcome to https://docs.milaboratories.com/
Based on our deep research of a large number of single-cell and molecular barcoded datasets, generated with dozens of protocols and instruments in a wide set of laboratory setups, we developed several important upgrades to the algorithms engaged in analysis of tagged data. With all the improvements and fixes, MiXCR 4.1 produces clean and reliable results for the majority of popular wet-lab protocols, being robust to a wide range of protocol noises, cross contamination mechanisms and artifacts. The set of tools offered by MiXCR 4.1 allows it to be applied for virtually any data of such type.
Featured fixes and upgrades:
assemblePartial
algorithm for tagged datarefineTagsAndSort
step (f/k/a correctAndSortTags
)refineTagsAndSort
)refineTagsAndSort
filtersassemble
); increased performance and stability in respect to data artifactsassemble
to fight cross-cell contaminationsassembleContigs
algorithm to increase robustness in respect to data artifactsMiXCR 4.1 introduces two new comprehensive tools for analysis of hypermutation trees of antibodies. The first is the de-novo discovery of V and J gene alleles provided by the findAlleles
command. And the second is the SHM trees reconstruction tool provided by the findShmTrees
command. These two features go hand in hand and help each other to accurately separate allelic variants from somatic mutations and reconstruct mutation tree topology, given the set of samples for the same individual. We implemented new original algorithms for these tasks, both are based on sophisticated analysis of alignments with germline segments, rather than naive reconstruction of mutation histories regardless of the sequence structure, as implemented in other tools. This functionality is accompanied by a set of commands to export SHM trees in several formats: exportShmTrees
, exportShmTreesWithNodes
, exportShmTreesNewick
and exportPlots shmTrees
.
findAlleles
and re-align all clonotype sequences (option -o
) to a newly generated individual reference V- and J-gene library.findAlleles
utilizes an allele inference algorithm which can use even somatically hypermutated clonal sequences as input data.findAlleles
and findShmTrees
commands support multiple .clns
files input - so the alleles can be inferred and lineage trees can be reconstructed using all available datasets. Note that it only makes sense to use datasets derived from an individual donor (or homogenic mouse strain) per command launch.From now on, most users can run the whole pipeline, specifying just a single option, the preset name, in addition to the input and output file names.
MiXCR provides tens of fine tuned sets of parameters (presets) to extract repertoires from the data generated with most of the commercially available kits and instruments as well as with the well established open protocols, including single-cell, bulk repertoire sequencing with or without molecular-barcodes and non-enriched data like RNA-Seq.
For example you can run the whole analysis (from fastq to clonesets) for the dataset generated with MiLaboratories Human TCR RNA Multiplex kit using the following command:
mixcr analyze milab-human-tcr-rna-multiplex-cdr3 input_file_R1.fastq.gz input_file_R2.fastq.gz results_prefix
This will produce a full set of intermediate files, with tsv clonesets and extensive report files both in txt
and json
formats.
The preset functionality is accompanied by the set of special high level command line options, we call mixins, that help to adapt the selected preset if experimental setup requires non-standard analysis (though it is not required in most cases).
The following improvements were made to MiXCR’s CLI:
analyze
command was completely redesigned (see example above)analyze
, align
or, for some mixins, on other pipeline stages{{a}}
and {{R}}
pattern elements added; now one can specify ... input_file_{{R}}.fastq.gz output.vdjca
instead of ... input_file_R1.fastq.gz input_file_R2.fastq.gz output.vdjca
MiXCR 4.1 introduces a new exportQc
command to visualize different quality control metrics including alignment performance, chain usage, reads coverage, barcode abundance distribution, automatically selected correction threshold etc.
biophysics
to cdr3metrics
in postanalysisexportPlots
--pairwise-comparisons
instead of --hide-pairwise-comparison
in exportPlots diversity / biophysics
--show-significance
option in exportPlots diversity / biophysics
exportClones
command multiple times (only “by chain” option is currently implemented)-tagFraction
)--not-aligned-R1/2
option for tagged analysis--not-parsed-R1/2
)--use-system-temp
assemble
report caused by pre-clone assembler which did not reported failed to extract target
--summary
option added to export downsampling statistics in a tabular form for mixcr downsample
sumWeightBefore/After
-uniqueTagFraction
pipelineInfo
command removed--palette
option added for plots (gene usage, overlap)-positionOf
export column (#699)--only-productive
in exportClonesOverlap
We also added many new unit and integration tests to keep the highest possible quality of the software at the same time allowing for the shorter release cycles.
correctAndSortTags
was renamed to refineTagsAndSort
-count
and -fraction
were renamed to -readCount
and -readFraction
correspondingly; column names in the tsv file has also changedanalyze
command was completely redesigned, and has no backward compatibility with previous parameters, however the same functionality can be achieved with generic-t(b)cr-amplicon
and rnaseq-tcr-cdr3
and similar presets (see the docs)See the following usage examples:
Set of powerful downstream analysis features with the ability to export postanalysis results in tabular format and vector plots with various statistical comparisons.
See the following usage guide:
Added command exportClonesOverlap
allowing to efficiently build and export overlap of the arbitrary number of clonesets.
See here for usage example.
MiXCR requires a license file to run. Academic users with no commercial funding can quickly obtain a MiXCR license for free at https://licensing.milaboratories.com/. We are committed to support academic community and provide our software free of charge for scientists doing non-profit research. Commercial trial license can be requested at https://licensing.milaboratories.com or by email to [email protected].
For details see: https://mixcr.com/mixcr/getting-started/milm/
assembleContigs
.analyze
doesn't use .clna
when contig assembly is not specifiedAlignConfiguration
to account for trimming--threads
option to analyze
--library
option to analyze
MiXCR is free for non-profit use only (see LICENSE for details)! For commercial use please contact [email protected].
mixcr
script optimizations for dockerMiXCR is free for non-profit use only (see LICENSE for details)! For commercial use please contact [email protected].
assemble
for multi-assembling-feature cases with zero length sequencesFR3
imputed sequence in cases with zero assembled nucleotides on the 5' side of CDR3Starting from this release we will maintain Official MiXCR Docker Image.
MiXCR is free for non-profit use only (see LICENSE for details)! For commercial use please contact [email protected].
NPE
in very rare cases with incompatible V gene selection for assembleContigs
in case of partially annotated gene librariesexportAlignments
/ exportClones
MiXCR is free for non-profit use only (see LICENSE for details)! For commercial use please contact [email protected].
split-by-V/J=true
casesalign
and assemble
JSON reports-nFeatureImputed ...
--json-report
= -j
analyze
parametersMiXCR is free for non-profit use only (see LICENSE for details)! For commercial use please contact [email protected].
-OaverageQualityThreshold=...
) in assembleContigs
increased to 20
exportAlignmentsForClones
actionassembleContigs
--trimming-window-size
and --trimming-quality-threshold
options in align
) (disabled by default until 3.1)-mutationsDetailed
and similar export optionsanalyze
(additional automatic parameter adjustment for VDJC libraries covering only VRegion
)assembleContigs
assemble
reportfilterAlignmentsAction
MiXCR is free for non-profit use only (see LICENSE for details)! For commercial use please contact [email protected].
CDR3
-OseparateByV=false
and similar overrides works with analyze shotgun
(issue #512)MiXCR is free for non-profit use only (see LICENSE for details)! For commercial use please contact [email protected].