Comments (4)
raissameyer
commented on September 25, 2024
Inferring taxonomy for metagenomes
Note
The names in the output of the following two commands is not the same as on the tutorial page Ribosomal_S6_2915 (Tutorial) Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_11655 (my output).
command
anvi-estimate-scg-taxonomy -c CONTIGS.db \
--metagenome-mode```
output
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| | percent_identity | taxonomy |
+==========================================================+====================+=================================================================================================================================+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_11655 | 98.9 | Bacteria / Firmicutes / Bacilli / Staphylococcales / Staphylococcaceae / Staphylococcus / Staphylococcus epidermidis |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_12163 | 98.9 | Bacteria / Firmicutes / Bacilli / Staphylococcales / Staphylococcaceae / Staphylococcus / Staphylococcus hominis |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_15200 | 98.9 | Bacteria / Firmicutes / Bacilli / Lactobacillales / Lactobacillaceae / Leuconostoc / Leuconostoc citreum |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_25880 | 98.9 | Bacteria / Firmicutes / Clostridia / Tissierellales / Peptoniphilaceae / Finegoldia / |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_2915 | 97.9 | Bacteria / Firmicutes / Bacilli / Lactobacillales / Enterococcaceae / Enterococcus / Enterococcus faecalis |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_29818 | 97.9 | Bacteria / Firmicutes / Bacilli / Lactobacillales / Streptococcaceae / Streptococcus / |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_30904 | 98.1 | Bacteria / Firmicutes / Clostridia / Tissierellales / Peptoniphilaceae / Anaerococcus / Anaerococcus nagyae |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_4484 | 98.9 | Bacteria / Firmicutes / Clostridia / Tissierellales / Peptoniphilaceae / Peptoniphilus / Peptoniphilus lacydonensis |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_6421 | 100 | Bacteria / Actinobacteriota / Actinomycetia / Propionibacteriales / Propionibacteriaceae / Cutibacterium / Cutibacterium avidum |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_7660 | 98.9 | Bacteria / Firmicutes / Bacilli / Staphylococcales / Staphylococcaceae / Staphylococcus / |
+----------------------------------------------------------+--------------------+---------------------------------------------------------------------------------------------------------------------------------+
command
anvi-estimate-scg-taxonomy -c CONTIGS.db \
> -p PROFILE.db \
> --metagenome-mode \
> --compute-scg-coverages
output
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| | percent_identity | taxonomy | DAY_15A | DAY_15B | DAY_16 | DAY_17A | DAY_17B | ... 6 more |
+==========================================================+====================+================================+===========+===========+==========+===========+===========+==============+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_2915 | 97.9 | (s) Enterococcus faecalis | 372.512 | 699.853 | 663.241 | 186.34 | 1149.6 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_11655 | 98.9 | (s) Staphylococcus epidermidis | 112.694 | 172.478 | 147.304 | 23.3901 | 140.769 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_4484 | 98.9 | (s) Peptoniphilus lacydonensis | 0 | 0 | 0 | 0 | 0 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_7660 | 98.9 | (g) Staphylococcus | 0 | 0 | 0 | 0 | 0 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_6421 | 100 | (s) Cutibacterium avidum | 17.8935 | 5.87368 | 4.79909 | 0 | 0 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_12163 | 98.9 | (s) Staphylococcus hominis | 2.39322 | 22.5447 | 13.2806 | 0 | 9.94853 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_15200 | 98.9 | (s) Leuconostoc citreum | 0 | 0 | 1.86532 | 0 | 1.6936 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_29818 | 97.9 | (g) Streptococcus | 0 | 0 | 0 | 0 | 0 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_25880 | 98.9 | (g) Finegoldia | 0 | 0 | 0 | 0 | 0 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
| Infant_Gut_Contigs_from_Sharon_et_al__Ribosomal_S6_30904 | 98.1 | (s) Anaerococcus nagyae | 0.528958 | 0 | 0.14157 | 0 | 0 | ... 6 more |
+----------------------------------------------------------+--------------------+--------------------------------+-----------+-----------+----------+-----------+-----------+--------------+
from merenlab.org.
raissameyer
commented on September 25, 2024
Manual identification of genomes in the Infant Gut Dataset
Note
For the manual identification of bins it would be helpful for the screenshot to include the information in the Bins tab (Len, Comp., Red.)
Image from tutorial
Image from my interface (please disregard that the bins I assigned are slightly different from the tutorial)
from merenlab.org.
raissameyer
commented on September 25, 2024
Chapter II: Automatic Binning
Manually curating automatic binning outputs
Note
Minor note, but I got a slightly different redundancy value than you report in the text (maxbin_007 has a redundancy value of 22% in the tutorial, 18.31% for me)
Text in tutorial
It is clear that some bins are not as well-resolved as others. For instance, bins maxbin_007 and maxbin_008 have redundancy estimates of 22% and 91%, respectively, which suggests each of them describe multiple distinct populations. Well, clearly we would have preferred those bins to behave.
command
anvi-estimate-genome-completeness -p PROFILE.db \
-c CONTIGS.db \
-C MAXBIN
my output
Bins in collection "MAXBIN"
===============================================
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| bin name | domain | confidence | % completion | % redundancy | num_splits | total length |
+============+==========+==============+================+================+==============+================+
| maxbin_001 | BACTERIA | 1 | 100 | 4.23 | 148 | 2969341 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_002 | BACTERIA | 1 | 94.37 | 0 | 88 | 1801068 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_003 | BACTERIA | 0.7 | 81.69 | 2.82 | 144 | 2764617 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_004 | BACTERIA | 1 | 97.18 | 1.41 | 188 | 2571878 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_005 | BACTERIA | 1 | 98.59 | 0 | 151 | 2555414 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_006 | BACTERIA | 0.7 | 78.87 | 5.63 | 305 | 2901149 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_007 | BACTERIA | 0.4 | 54.93 | 18.31 | 724 | 3230717 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_008 | BACTERIA | 0.8 | 87.32 | 90.14 | 1657 | 3056818 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
| maxbin_009 | EUKARYA | 0.8 | 83.13 | 7.23 | 1379 | 13915165 |
+------------+----------+--------------+----------------+----------------+--------------+----------------+
from merenlab.org.
ivagljiva
commented on September 25, 2024
Thanks for the heads up on these issues @raissameyer :) I started a branch (IGT_fixes_from_Raissa) and fixed the table outputs. I didn't want to update the binning screenshot myself since it has nice colors, so I leave that one to @metehaansever :)
from merenlab.org.
Related Issues (6)
- minor blog issues HOT 1
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