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Next development cycle v2.1.3

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dbolotin committed Aug 22, 2018
1 parent c392439 commit 13529a27b04063b4ae565c2f852c7f58a66084c1
Showing with 2,409 additions and 574 deletions.
  1. +8 −0 CHANGELOG
  2. +4 −4 LICENSE
  3. +104 −0 doc/BaseSpaceApp.rst
  4. +116 −56 doc/align.rst
  5. +42 −0 doc/appendix.rst
  6. +63 −1 doc/assemble.rst
  7. +4 −4 doc/conf.py
  8. +2 −0 doc/export.rst
  9. +2 −2 doc/install.rst
  10. +1 −1 doc/rnaseq.rst
  11. +5 −4 pom.xml
  12. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java
  13. +356 −0 src/main/java/com/milaboratory/mixcr/assembler/AlignmentsToClonesMappingContainer.java
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  15. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java
  16. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java
  17. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java
  18. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java
  19. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java
  20. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java
  21. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java
  22. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java
  23. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java
  24. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java
  25. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java
  26. +6 −4 src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java
  27. +9 −7 src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java
  28. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java
  29. +29 −0 src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java
  30. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java
  31. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java
  32. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java
  33. +4 −3 src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java
  34. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java
  35. +29 −0 src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java
  36. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/Clone.java
  37. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java
  38. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java
  39. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java
  40. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java
  41. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java
  42. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/IO.java
  43. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java
  44. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/Merger.java
  45. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/RandomAccessVDJCAReader.java
  46. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java
  47. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java
  48. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
  49. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java
  50. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java
  51. +29 −0 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java
  52. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java
  53. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java
  54. +4 −3 src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java
  55. +4 −3 src/main/java/com/milaboratory/mixcr/cli/AbstractActionReport.java
  56. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java
  57. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ActionAlignmentsDiff.java
  58. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionAlignmentsStat.java
  59. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionAssemble.java
  60. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ActionAssemblePartialAlignments.java
  61. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionClonesDiff.java
  62. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionExport.java
  63. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionExportAlignments.java
  64. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionExportAlignmentsPretty.java
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  66. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionExportClones.java
  67. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionExportClonesPretty.java
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  69. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionExportReads.java
  70. +176 −0 src/main/java/com/milaboratory/mixcr/cli/ActionExtendAlignments.java
  71. +29 −0 src/main/java/com/milaboratory/mixcr/cli/ActionFilterAlignments.java
  72. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionInfo.java
  73. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionListLibraries.java
  74. +4 −3 src/main/java/com/milaboratory/mixcr/cli/ActionMergeAlignments.java
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  88. +4 −3 src/main/java/com/milaboratory/mixcr/export/AbstractField.java
  89. +4 −3 src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java
  90. +29 −0 src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
  91. +4 −3 src/main/java/com/milaboratory/mixcr/export/Field.java
  92. +4 −3 src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java
  93. +4 −3 src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java
  94. +4 −3 src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java
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  97. +4 −3 src/main/java/com/milaboratory/mixcr/export/InfoWriter.java
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  99. +4 −3 src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java
  100. +4 −3 src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java
  101. +4 −3 src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java
  102. +4 −3 src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java
  103. +4 −3 src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java
  104. +4 −3 src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java
  105. +30 −1 src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java
  106. +4 −3 src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java
  107. +4 −3 src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java
  108. +4 −3 src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java
  109. +29 −0 src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java
  110. +4 −3 src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java
  111. +4 −3 src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java
  112. +29 −0 src/main/java/com/milaboratory/mixcr/util/PositiveLongValidator.java
  113. +4 −3 src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java
  114. +29 −0 src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java
  115. +29 −0 src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java
  116. +29 −0 src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java
  117. +29 −0 src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java
  118. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java
  119. +29 −0 src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java
  120. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java
  121. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java
  122. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java
  123. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java
  124. +81 −10 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java
  125. +12 −11 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java
  126. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java
  127. +7 −61 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java
  128. +8 −7 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java
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  130. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java
  131. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java
  132. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java
  133. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java
  134. +4 −3 src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java
  135. +124 −0 src/test/java/com/milaboratory/mixcr/assembler/AlignmentsToClonesMappingContainerTest.java
  136. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java
  137. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java
  138. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java
  139. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java
  140. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java
  141. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java
  142. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java
  143. +4 −3 src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java
  144. +4 −3 src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java
  145. +4 −3 src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java
  146. +4 −3 src/test/java/com/milaboratory/mixcr/basictypes/MergerTest.java
  147. +4 −3 src/test/java/com/milaboratory/mixcr/basictypes/RandomAccessVDJCAReaderTest.java
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  155. +4 −3 src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java
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  167. +4 −3 src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java
  168. +4 −3 src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java
  169. +4 −3 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java
  170. +4 −3 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java
  171. +4 −3 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java
  172. +4 −3 src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java
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View
@@ -1,4 +1,12 @@
MiXCR 2.1.12 (22 Aug 2018)
========================
-- Fixes rare inconsistency in behaviour between paired-end and single-end aligners, clone
assembler and partial sequence assembler in respect to target D gene set selection based on the
chains on V, J and C genes (#408)
MiXCR 2.1.11 (15 Jun 2018)
========================
View
@@ -1,4 +1,4 @@
Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
(here and after addressed as Inventors)
All Rights Reserved
@@ -9,8 +9,8 @@ provided that the above copyright notice, this paragraph and the following
three paragraphs appear in all copies.
Those desiring to incorporate this work into commercial products or use for
commercial purposes should contact MiLaboratory LLC, which owns exclusive
rights for distribution of this program for commercial purposes, using the
commercial purposes should contact MiLaboratory LLC, which owns exclusive
rights for distribution of this program for commercial purposes, using the
following email address: licensing@milaboratory.com.
IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
@@ -24,4 +24,4 @@ MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO
WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY
PATENT, TRADEMARK OR OTHER RIGHTS.
PATENT, TRADEMARK OR OTHER RIGHTS.
View
@@ -0,0 +1,104 @@
.. |br| raw:: html
<br />
.. _ref-basespace:
MiXCR Immune Repertoire Analyzer @ BaseSpace®
=============================================
If your data is deposited at the BaseSpace cloud platform you can perform repertoire extraction and calculate common analysis metrics like V/J usage, without leaving BaseSpace UI. MiXCR Immune Repertoire Analyzer app is available for all BaseSpace users (this `link <https://basespace.illumina.com/apps/5538533/MiXCR-Immune-Repertoire-Analyzer>`_ works if you are logged in into base space, and `this one <https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/milaboratory-mixcr-immune-repertoire-analyzer.html>`_ points to the overview page available without authentication).
Input
-----
User interface of MiXCR Immune Repertoire Analyzer was specifically optimized to set up best possible analysis pipeline with the minimal possible set of parameters, covering majority of the sequencing data types, TCR/IG repertoires can be extracted from.
The list of possible sequencing material sources include, but is not limited to:
- all targeted TCR and IG profiling protocols (both RNA- and gDNA-derived, including multiplex-PCR and 5'RACE based techniques)
- non-enriched RNA-Seq data
- WGS
- single-cell data
Parameters
----------
Starting material
^^^^^^^^^^^^^^^^^
Sets the type of starting material (RNA or Genomic DNA) of the library. This determines whether MiXCR will look for V introns.
Library type
^^^^^^^^^^^^
This option determines whether the data will be treated as amplicon library with the same relative sequence architecture across all reads, where CDR3 is fully covered by each read. Or, randomly shred library like RNA-Seq or WGS, so MiXCR will perform assembly of target molecules from several reads.
"Random fragments" option works well for shallow libraries like RNA-Seq of solid tissue or sorted cell populations, but if the library is too reach with the target molecules (e.g. library was additionally enriched using bait probes), using this option may drastically degrade both computational and "analytical" performance. In this case, select "Targeted TCR/IG library", no partial CDR3 assembly will be performed, still, sequences extracted from reads with full CDR3 coverage, should be enough for the analysis.
Targeted Library Parameters: 5’-end of the library
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you specify the library may contain V primer sequence on the 5' end, and it was not trimmed (see "Presence of PCR primers and/or adapter sequences"), alignment of V genes will not be forcefully extended to the left side and clonotypes with the same clonal sequence (specified in "Target region") but different V gene will not be separated into individual records.
Primers for some segments if accidentally annealed to non-target region may introduce chimeric sequences, and prevent exact V gene assignment, thus generating artificial clonotypes differing by only V gene assigned. Clonotype splitting by V gene is turned off to prevent generation of this type of artificial diversity.
Targeted Library Parameters: 3’-end of the library
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you specify the library may contain J or C primer sequence on the 3' end, and it was not trimmed (see "Presence of PCR primers and/or adapter sequences"), alignment of J or C genes respectively will not be forcefully extended to the right side, and clonotypes with the same clonal sequence (specified in "Target region") but different J or C gene will not be separated into individual records (the motivation is the same as for 5’-end).
Presence of PCR primers and/or adapter sequences
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Specifies whether the adapter and primer sequences were trimmed for this data. This applies to V/J/C primers, 5'RACE adapters or nay other sequence not originating from target molecules.
It affects V/J/C alignment parameters (see above), and also affects alignment of V 5'UTR sequence (5'UTR will not be aligned if sequence may contain 5'RACE adapter sequences, e.g. if 5’-end of the library do not contain primer sequence is not marked as containing primer, but "Presence of PCR primers and/or adapter sequences" is set to "May be present".
Analysis Settings
-----------------
Target region
^^^^^^^^^^^^^
Region of the sequence to assemble clones by. Only this part of the sequence will be available in the output.
Filter
^^^^^^
**Filter out-of-frame CDR3s** Output only in-frame reads
**Filter out CDR3s with stop codon** Don't output sequences containing stop codons in their target region.
Output
^^^^^^
Specify which immunological chains you are interested in. Regardless of the values specified here, data will be aligned against all chains.
Hidden parameters
-----------------
All other parameters, like parameters for error correction algorithms, parameters for partial CDR3 reconstruction, extension, etc. are set to their default values, optimal in most cases.
Output
------
MiXCR Immune Repertoire Analyzer produces tab separated tables containing comprehensive information about clonotypes detected during analysis. This information includes:
- Clonal sequence
- Aggregated quality score values for clonal sequence
- Anchor positions inside clonal sequence
- Assigned V/D/J/C genes, among with corresponding aggregated alignment scoring
- Encoded alignments of V/J/C genes inside clonal sequence
MiXCR Immune Repertoire Analyzer also contains useful statistics and corresponding charts for the clonesets produced with `VDJTools <https://github.com/mikessh/vdjtools>`_ .
Graphical output is available for:
- Overall analysis statistics: total number of processed sequence, successfully aligned sequences, and number of sequences passed different clonotype assembling stages
- V and J usage
- Spectratype, marked with major clonotypes
- Spectratype, marked with V gene usage
- Quantile statistics
- And the table of top clonotypes marked wit V, D and J genes
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