`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

.txt.json

============== 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

assemblePartial report

`assemblePartial` report