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assemblePartial report

MiXCR generates a comprehensive summary of partial assembly performance. Assemble reports may be generated right along with assemblePartial 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
============== AssemblePartial Report ==============
Analysis date: Thu Jul 28 11:51:13 CEST 2022
Input file(s): clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca
Output file(s): clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca
Version: ; built=Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; lib=repseqio.v2.0
Command line arguments: assemblePartial -f --report clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.txt -j clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.json clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca
Analysis time: 12.71m
Independent runs: 118472787
Total alignments analysed: 118472787
Number of output alignments: 118169463 (99.74%)
Alignments already with CDR3 (no overlapping is performed): 5420162 (4.58%)
Successfully overlapped alignments: 302715 (0.26%)
Left parts with too small N-region (failed to extract k-mer): 4530050 (3.82%)
Extracted k-mer diversity: 19607617
Dropped due to wildcard in k-mer: 0 (0%)
Dropped due to too short NRegion parts in overlap: 51841 (0.04%)
Dropped overlaps with empty N region due to no complete NDN coverage: 3958 (0%)
Number of left-side alignments: 1835970 (1.55%)
Number of right-side alignments: 3167157 (2.67%)
Complex overlaps: 0 (0%)
Over-overlaps: 197 (0%)
Partial alignments written to output: 112446586 (94.91%)
{
  "type": "partialAlignmentsAssemblerReport",
  "commandLine": "assemblePartial -f --report clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.txt -j clones_newMiXcr/Donor1_MBC_2010_assemblePartialReport.json clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca",
  "inputFiles": [
    "clones_newMiXcr/Donor1_MBC_2010_corrected.vdjca"
  ],
  "outputFiles": [
    "clones_newMiXcr/Donor1_MBC_2010_partialAssemble.vdjca"
  ],
  "version": "; built=Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; lib=repseqio.v2.0",
  "independentRuns": 6478545,
  "totalProcessed": 118472787,
  "outputAlignments": 118169463,
  "withCDR3": 5420162,
  "overlapped": 302715,
  "leftTooShortNRegion": 4530050,
  "kMerDiversity": 19607617,
  "droppedWildcardsInKMer": 0,
  "droppedSmallOverlapNRegion": 51841,
  "droppedNoNRegion": 3958,
  "leftParts": 1835970,
  "rightParts": 3167157,
  "complexOverlaps": 0,
  "overOverlaps": 197,
  "partialAlignmentsAsIs": 112446586
}
Independent runs
Number of independent assemblePartial rounds
Total alignments analysed
Number of total input alignments
Number of output alignments
Number of total output alignments
Alignments already with CDR3 (no overlapping is performed)
Number of input alignments that already covered CDR3
Successfully overlapped alignments
Number of overlapped alignments
Left parts with too small N-region (failed to extract k-mer)
Number of left alignments with too small N-region (not enough entropy to assign to a unique molecule)
Extracted k-mer diversity
Number of different k-mers
Dropped due to wildcard in k-mer
Dropped alignments due wildcards in k-mers
Dropped due to too short NRegion parts in overlap
Dropped due too small number of N letters in overlap (not enough entropy to assign to a unique molecule)
Dropped overlaps with empty N region due to no complete NDN coverage
Dropped due absent N letters in overlap (not enough entropy to assign to a unique molecule)
Number of left-side alignments
Number of left alignments
Number of right-side alignments
Number of right alignments
Complex overlaps
Multiple overlaps for same molecule
Over-overlaps
Over overlaped alignments
Partial alignments written to output
Partial (no full CDR3) alignments written to output