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Young edited this page Feb 23, 2024 · 2 revisions

Blobtools

About: |

A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

At UPHL we use it to detect inter-species contamination.

Documentation : https://github.com/DRL/blobtools

Citation : https://f1000research.com/articles/6-1287/v1

Directory tree:

blobtools
├── blobtools_summary.txt
├── sample.blobDB.json
├── sample.blobDB.json.bestsum.species.p8.span.100.blobplot.bam0.png
├── sample.blobDB.json.bestsum.species.p8.span.100.blobplot.read_cov.bam0.png
├── sample.blobDB.json.bestsum.species.p8.span.100.blobplot.stats.txt
├── sample.blobDB.table.txt
├── sample_blobtools.txt
├── sample.sample.sr.bam.cov
└── sample_summary.txt

Example file for an individual sample (sample.blobDB.json.bestsum.species.p8.span.100.blobplot.stats.txt)

## 1.1.1
## bam0=/Volumes/IDGenomics_NAS/Bioinformatics/eriny/testing_grandeur/2024-02-21/work/17/41683b71d511ce812747b2c982ddbb/SRR14436834.sr.bam
# name  colour  count_visible   count_visible_perc      span_visible    span_visible_perc       n50     gc_mean gc_std  bam0_mean     bam0_std bam0_read_map   bam0_read_map_p
all     None    485     99.0%   4,697,009       100.0%  17,852  0.67    0.029   34.8    13.9    817,956 98.3%
undef   #1f77b4 473     99.4%   4,656,431       100.0%  17,655  0.67    0.028   34.9    13.8    812,393 97.7%
Stenotrophomonas pavanii        #ff7f0e 1       100.0%  33,768  100.0%  33,768  0.62    0.0     29.0    0.0     4,491   0.5%
Stenotrophomonas maltophilia    #d62728 8       88.9%   3,619   97.4%   614     0.63    0.029   35.4    19.4    681     0.1%
Bordetella hinzii       #9467bd 1       100.0%  2,667   100.0%  2,667   0.59    0.0     26.9    0.0     329     0.0%
no-hit  #d3d3d3 1       50.0%   332     81.0%   332     0.54    0.0     21.0    0.0     32      0.0%
Thauera linaloolentis   #e377c2 1       100.0%  192     100.0%  192     0.62    0.0     34.1    0.0     30      0.0%

blobtools also creates images. These images are not included in multiQC because there are too many of them.

sample.blobDB.json.bestsum.species.p8.span.100.blobplot.bam0.png SRR11725329 blobDB json bestsum species p8 span 100 blobplot bam0

sample.blobDB.json.bestsum.species.p8.span.100.blobplot.read_cov.bam0.png SRR11725329 blobDB json bestsum species p8 span 100 blobplot read_cov bam0

Example file for a run (blobtools_summary.txt)

sample  name    colour  count_visible   count_visible_perc      span_visible    span_visible_perc       n50     gc_mean gc_std  bam0_mean      bam0_std        bam0_read_map   bam0_read_map_p
82300018-UT-M70330-230725       all     None    771     100.0   6,330,471       100.0   31,336  0.36    0.048   109.9   243.4   1,340,349      98.0
82300018-UT-M70330-230725       undef   #1f77b4 208     100.0   3,058,876       100.0   36,415  0.36    0.036   62.0    82.6    521,37438.1
82300018-UT-M70330-230725       Bacillus_thuringiensis  #d62728 114     100.0   1,086,304       100.0   27,925  0.37    0.041   145.9 277.5    223,150 16.3
82300018-UT-M70330-230725       Bacillus_cereus #ff7f0e 67      100.0   1,402,306       100.0   34,647  0.35    0.032   31.2    15.0  183,955  13.5
82300018-UT-M70330-230725       other   #ffffff 74      100.0   235,255 100.0   9,845   0.38    0.062   247.9   498.4   134,176 9.8
82300018-UT-M70330-230725       Bacillus_sp._ATCC_21929 #9467bd 54      100.0   162,092 100.0   12,756  0.35    0.029   114.5   140.0 73,622   5.4
82300018-UT-M70330-230725       no-hit  #d3d3d3 199     100.0   102,338 100.0   841     0.36    0.063   112.9   256.0   72,139  5.3
SRR11725329     all     None    185     100.0   5,286,834       100.0   334,258 0.53    0.062   74.4    291.7   1,085,132       99.5
SRR11725329     Shigella_boydii #1f77b4 7       100.0   2,408,978       100.0   470,112 0.51    0.012   43.0    12.8    479,076 43.9
SRR11725329     Escherichia_coli        #ff7f0e 37      100.0   2,007,183       100.0   203,690 0.52    0.04    59.7    58.6    408,26837.4
SRR11725329     undef   #d62728 67      100.0   447,818 100.0   96,073  0.54    0.05    129.4   476.3   138,024 12.7
SRR13643280     all     None    160     100.0   3,908,943       100.0   94,742  0.42    0.087   67.7    163.5   1,052,866       99.5
SRR13643280     Acinetobacter_baumannii #1f77b4 86      100.0   3,397,807       100.0   94,742  0.4     0.048   60.2    42.6    888,36283.9
SRR13643280     undef   #ff7f0e 31      100.0   201,621 100.0   107,553 0.46    0.088   126.3   352.6   83,478  7.9
SRR14436834     all     None    485     99.0    4,697,009       100.0   17,852  0.67    0.029   34.8    13.9    817,956 98.3
SRR14436834     undef   #1f77b4 473     99.4    4,656,431       100.0   17,655  0.67    0.028   34.9    13.8    812,393 97.7
SRR14634837     all     None    160     100.0   5,709,554       100.0   294,187 0.53    0.082   60.5    75.8    1,184,605       99.5
SRR14634837     Klebsiella_pneumoniae   #1f77b4 42      100.0   5,279,577       100.0   294,187 0.56    0.035   48.3    26.6    1,074,361      90.3
SRR7738178      all     None    752     100.0   4,809,771       100.0   25,896  0.49    0.057   80.5    469.5   990,400 97.0
SRR7738178      Escherichia_coli        #1f77b4 305     100.0   3,934,428       100.0   27,726  0.5     0.046   44.4    67.8    688,73967.4
SRR7738178      undef   #ff7f0e 107     100.0   234,168 100.0   16,527  0.51    0.048   193.2   1053.9  103,695 10.2
SRR7738178      other   #ffffff 75      100.0   98,622  100.0   7,973   0.49    0.1     125.0   653.1   91,579  9.0
SRR7738178      Streptococcus_sp._28462 None    2       100.0   2,656   100.0   2,216   0.47    0.0033  2783.1  2780.4  51,441  5.0
SRR7889058      all     None    96      100.0   4,754,434       100.0   525,710 0.53    0.076   56.8    85.6    1,131,246       98.2
SRR7889058      Salmonella_enterica     #1f77b4 45      100.0   4,734,657       100.0   525,710 0.53    0.061   46.0    55.2    1,112,662      96.6
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