2024.09 #3433
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2024.09 #3433
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antgonza
commented
Sep 12, 2024
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| Wolka and Bowtie2 using Read Pairing Schemes | |||
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@qiyunzhu; could you take a look? Thank you.
charles-cowart
approved these changes
Sep 12, 2024
| The bowtie2 settings are maximum and minimum mismatch penalties (mp=[1,1]), a | ||
| penalty for ambiguities (np=1; default), read and reference gap open- and | ||
| The bowtie2 settings are set for interleaved processing with a maximum and minimum mismatch | ||
| penalties (mp=[1,1]), a penalty for ambiguities (np=1; default), read and reference gap open- and |
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"reference gap open- and" seems odd. Perhaps it should be "open-and"? or maybe the hyphen should be removed?
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| Here I tested alternative read pairing schemes in the analysis of shotgun metagenomic sequencing data. Sequencing reads were aligned against a reference microbial genome database as unpaired or paired, with or without singleton and/or discordant alignments suppressed. A series of synthetic datasets were used in the analysis. | ||
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| The results reveal that treating reads as paired is always advantageous over unpaired. Suppressing singleton alignments further increases the accuracy of results, despite at the cost of lower mapping rate. Suppressing discordant alignments has no obvious impact on the result. Regardless of accuracy, the downstream community ecology analyses are not obviously impacted by the choice of parameters. |
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despite at the cost -> despite the cost
| Summary | ||
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| Here I tested alternative read pairing schemes in the analysis of shotgun metagenomic sequencing data. Sequencing reads were aligned against a reference microbial genome database as unpaired or paired, with or without singleton and/or discordant alignments suppressed. A series of synthetic datasets were used in the analysis. |
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Here I tested -> I tested
charles-cowart
approved these changes
Sep 12, 2024
qiyunzhu
reviewed
Sep 12, 2024
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| - Mapping rate (%) | ||
| - Number of taxa | ||
| - Entropy (i.e., Shannon index, but without subsampling) |
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This line (37) can be removed. Also replace "three" with "two" in line 33.
| Summary | ||
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| I tested alternative read pairing schemes in the analysis of shotgun metagenomic sequencing data. Sequencing reads were aligned against a reference microbial genome database as unpaired or paired, with or without singleton and/or discordant alignments suppressed. A series of synthetic datasets were used in the analysis. |
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"singleton and/or discordant alignments" is now irrelevant. It needs to be removed from this paragraph and the next two.
| Alignment parameters | ||
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| Sequencing data were aligned using Bowtie2 v2.5.1 in the “very sensitive” mode against the WoL2 database. They were treated as either unpaired or paired-end: |
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Double quotes may be replaced with "?
| #. PE outperforms SE in all metrics. Most importantly, it reduces false positive rate (higher precision) while retaining mapping rate. Meanwhile, the sensitivity (recall) of identifying true taxa is not obviously compromised (note the y-axis scale). | ||
| #. PE.NU the two additional parameters had minimum effect on the result and make the alignment step faster. This may suggest that the additional parameters are safe to use. | ||
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| Therefore, I would recommend adopting paired alignment in preference to unpaired alignment. I may suggest no mixing as it has improved accuracy, but the potential adverse effect of lower mapping rate may be further explored before making a compelling recommendation. Although not having a visible effect, no discordance may be added for logical coherency. |
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Can remove "no mixing... no discordance".
| * Initial changes in `qiita_client` to have more accurate variable names: `QIITA_SERVER_CERT` -> `QIITA_ROOTCA_CERT`. Thank you @charles-cowart! | ||
| * Added `get_artifact_html_summary` to `qiita_client` to retrieve the summary file of an artifact. | ||
| * Re-added github actions to `https://github.com/qiita-spots/qiita_client`. | ||
| * `Woltka v0.1.4, paired-end` superseded `Woltka v0.1.4` in `qp-woltka`; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/woltka_pairedend.html). Thank you to @qiyunzhu for the benchmarks! |
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Should upgrade Woltka to v0.1.6. (!important!)
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