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assembleContigs report

MiXCR generates a comprehensive summary of contig assembly performance. Assemble reports may be generated right along with assembleContigs command using -r/--report for txt report and -j/--json-report for report in a json format, or can be exported using exportReports command.

Show sample report 
============== AssembleContigs Report ==============
Analysis date: Mon Jul 11 10:46:49 CEST 2022
Input file(s): result/Donor1_MBC_2010.clna
Output file(s): result/Donor1_MBC_2010.clns
Version: unspecified; built=Mon Jul 04 17:40:12 CEST 2022; rev=8faa71789a; lib=repseqio.v2.0
Command line arguments: assembleContigs -r result/Donor1_MBC_2010_assembleContigsReport.txt -f result/Donor1_MBC_2010.clna result/Donor1_MBC_2010.clns
Analysis time: 2.09s
Initial clonotype count: 1784
Final clonotype count: 1784 (100%)
Canceled assemblies: 0 (0%)
Number of premature termination assembly events, percent of number of initial clonotypes: 0.0 (0%)
Longest contig length: 303
Clustered variants: 0 (0%)
Reads in clustered variants: 0.0 (0%)
Reads in divided (newly created) clones: 0.0 (0%)
Clones with ambiguous letters in splitting region: 0 (0%)
Reads in clones with ambiguous letters in splitting region: 0.0 (0%)
Average number of ambiguous letters per clone with ambiguous letters in splitting region: NaN

{
  "type": "fullSeqAssemblerReport",
  "commandLine": "assembleContigs -r result/Donor1_MBC_2010_assembleContigsReport.txt -j result/Donor1_MBC_2010_assembleContigsReport.json -f result/Donor1_MBC_2010.clna result/Donor1_MBC_2010.clns",
  "inputFiles": [
    "result/Donor1_MBC_2010.clna"
  ],
  "outputFiles": [
    "result/Donor1_MBC_2010.clns"
  ],
  "version": "; built=Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; lib=repseqio.v2.0",
  "clonesWithAmbiguousLetters": 85,
  "clonesWithAmbiguousLettersInSplittingRegion": 0,
  "readsWithAmbiguousLetters": 296,
  "readsWithAmbiguousLettersInSplittingRegion": 0,
  "totalAmbiguousLetters": 185,
  "totalAmbiguousLettersInSplittingRegion": 0,
  "initialCloneCount": 1784,
  "canceledAssemblies": 0,
  "finalCloneCount": 1784,
  "totalReadsProcessed": 2723,
  "clonesClustered": 0,
  "readsClustered": 0,
  "longestContigLength": 303,
  "totalDividedVariantReads": 0,
  "assemblePrematureTerminationEvents": 0
}
Initial clonotype count
Number of input clonotypes
Final clonotype count
Number of final clonotypes (may be greater than initial number if -OsubCloningRegion is specified)
Canceled assemblies
Number of skipped clonotypes
Number of premature termination assembly events, percent of number of initial clonotypes
Number of cancelled assemblies due to no hits on the final clone factory step
Longest contig length
Length of the longest contig
Clustered variants
Number of clusterized variant branches
Reads in clustered variants
Number of reads in clustered variants
Reads in divided (newly created) clones
Number of reads in the newly created clones (if -OsubCloningRegion is specified and hypermutated variants discovered)
Clones with ambiguous letters in splitting region
Number of clonotypes with ambiguous letters inside subCloningRegion (MiXCR will use Ns for such letters)
Reads in clones with ambiguous letters in splitting region
Number of reads in such ambiguous clonotypes
Average number of ambiguous letters per clone with ambiguous letters in splitting region
Average number of ambiguous letters per clone with ambiguous letters in splitting region