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kaijli committed Nov 21, 2024
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53 changes: 34 additions & 19 deletions README.rst
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Expand Up @@ -11,7 +11,9 @@ The pipeline takes in sequencing files (single- or paired-end) and profiles them

Workflow Availability
---------------------
The workflow is available in GitHub: https://github.com/microbiomedata/ReadbasedAnalysis; the corresponding Docker image is available in DockerHub: https://hub.docker.com/r/microbiomedata/nmdc_taxa_profilers
The workflow is available in GitHub: https://github.com/microbiomedata/ReadbasedAnalysis; the corresponding Docker image is available in DockerHub:

- `microbiomedata/nmdc_taxa_profilers: <https://hub.docker.com/r/microbiomedata/nmdc_taxa_profilers>`_

Requirements for Execution:
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -81,12 +83,12 @@ Sample dataset(s):

- Soil microbial communities from the East River watershed near Crested Butte, Colorado, United States - ER_DNA_379 metagenome (`SRR8553641 <https://www.ncbi.nlm.nih.gov/sra/SRX5355418>`) with `metadata available in the NMDC Data Portal <https://data.microbiomedata.org/details/study/nmdc:sty-11-dcqce727>`_. This dataset has 18.3G bases

- The zipped raw fastq file is available `here <https://portal.nersc.gov/project/m3408//test_data/SRR8553641/SRR8553641.fastq.gz>`_
- The zipped raw fastq file is available `here <https://portal.nersc.gov/project/m3408//test_data/SRR8553641/SRR8553641.fastq.gz>`_

- Zymobiomics mock-community DNA control (`SRR7877884 <https://www.ncbi.nlm.nih.gov/sra/SRX4716743>`_); this dataset is has 6.7G bases.

- The non-interleaved raw fastq files are available as `R1 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_1.fastq.gz>`_ and `R2 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_2.fastq.gz>`
- The interleaved raw fastq file is available `here <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884-int.fastq.gz>`_
- The non-interleaved raw fastq files are available as `R1 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_1.fastq.gz>`_ and `R2 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_2.fastq.gz>`
- The interleaved raw fastq file is available `here <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884-int.fastq.gz>`_

Input: A JSON file containing the following information:

Expand Down Expand Up @@ -123,7 +125,9 @@ Input: A JSON file containing the following information:
Output:
~~~~~~~

The workflow creates an output JSON file and individual output sub-directories for each tool which include tabular classification results, a tabular report, and a Krona plot (html).::
The workflow creates an output JSON file and individual output sub-directories for each tool which include tabular classification results, a tabular report, and a Krona plot (html).

::

ReadbasedAnalysis/
|-- SRR7877884.json
Expand All @@ -145,20 +149,31 @@ The workflow creates an output JSON file and individual output sub-directories f

Below is an example of the output directory files with descriptions to the right.

======================================== ==============================================
FileName Description
---------------------------------------- ----------------------------------------------
SRR7877884.json ReadbasedAnalysis result JSON file
centrifuge/SRR7877884.classification.tsv Centrifuge output read classification TSV file
centrifuge/SRR7877884.report.tsv Centrifuge output report TSV file
centrifuge/SRR7877884.krona.html Centrifuge krona plot HTML file
gottcha2/SRR7877884.full.tsv GOTTCHA2 detail output TSV file
gottcha2/SRR7877884.tsv GOTTCHA2 output report TSV file
gottcha2/SRR7877884.krona.html GOTTCHA2 krona plot HTML file
kraken2/SRR7877884.classification.tsv Kraken2 output read classification TSV file
kraken2/SRR7877884.report.tsv Kraken2 output report TSV file
kraken2/SRR7877884.krona.html Kraken2 krona plot HTML file
======================================== ==============================================
.. list-table::
:header-rows: 1

* - Directory/File Name
- Description
* - SRR7877884.json
- ReadbasedAnalysis result JSON file
* - centrifuge/SRR7877884.classification.tsv
- Centrifuge output read classification TSV file
* - centrifuge/SRR7877884.report.tsv
- Centrifuge output report TSV file
* - centrifuge/SRR7877884.krona.html
- Centrifuge krona plot HTML file
* - gottcha2/SRR7877884.full.tsv
- GOTTCHA2 detail output TSV file
* - gottcha2/SRR7877884.tsv
- GOTTCHA2 output report TSV file
* - gottcha2/SRR7877884.krona.html
- GOTTCHA2 krona plot HTML file
* - kraken2/SRR7877884.classification.tsv
- Kraken2 output read classification TSV file
* - kraken2/SRR7877884.report.tsv
- Kraken2 output report TSV file
* - kraken2/SRR7877884.krona.html
- Kraken2 krona plot HTML file


Version History
Expand Down
53 changes: 34 additions & 19 deletions docs/index.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,9 @@ The pipeline takes in sequencing files (single- or paired-end) and profiles them

Workflow Availability
---------------------
The workflow is available in GitHub: https://github.com/microbiomedata/ReadbasedAnalysis; the corresponding Docker image is available in DockerHub: https://hub.docker.com/r/microbiomedata/nmdc_taxa_profilers
The workflow is available in GitHub: https://github.com/microbiomedata/ReadbasedAnalysis; the corresponding Docker image is available in DockerHub:

- `microbiomedata/nmdc_taxa_profilers: <https://hub.docker.com/r/microbiomedata/nmdc_taxa_profilers>`_

Requirements for Execution:
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -81,12 +83,12 @@ Sample dataset(s):

- Soil microbial communities from the East River watershed near Crested Butte, Colorado, United States - ER_DNA_379 metagenome (`SRR8553641 <https://www.ncbi.nlm.nih.gov/sra/SRX5355418>`) with `metadata available in the NMDC Data Portal <https://data.microbiomedata.org/details/study/nmdc:sty-11-dcqce727>`_. This dataset has 18.3G bases

- The zipped raw fastq file is available `here <https://portal.nersc.gov/project/m3408//test_data/SRR8553641/SRR8553641.fastq.gz>`_
- The zipped raw fastq file is available `here <https://portal.nersc.gov/project/m3408//test_data/SRR8553641/SRR8553641.fastq.gz>`_

- Zymobiomics mock-community DNA control (`SRR7877884 <https://www.ncbi.nlm.nih.gov/sra/SRX4716743>`_); this dataset is has 6.7G bases.

- The non-interleaved raw fastq files are available as `R1 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_1.fastq.gz>`_ and `R2 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_2.fastq.gz>`
- The interleaved raw fastq file is available `here <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884-int.fastq.gz>`_
- The non-interleaved raw fastq files are available as `R1 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_1.fastq.gz>`_ and `R2 <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884_2.fastq.gz>`
- The interleaved raw fastq file is available `here <https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884-int.fastq.gz>`_

Input: A JSON file containing the following information:

Expand Down Expand Up @@ -123,7 +125,9 @@ Input: A JSON file containing the following information:
Output:
~~~~~~~

The workflow creates an output JSON file and individual output sub-directories for each tool which include tabular classification results, a tabular report, and a Krona plot (html).::
The workflow creates an output JSON file and individual output sub-directories for each tool which include tabular classification results, a tabular report, and a Krona plot (html).

::

ReadbasedAnalysis/
|-- SRR7877884.json
Expand All @@ -145,20 +149,31 @@ The workflow creates an output JSON file and individual output sub-directories f

Below is an example of the output directory files with descriptions to the right.

======================================== ==============================================
FileName Description
---------------------------------------- ----------------------------------------------
SRR7877884.json ReadbasedAnalysis result JSON file
centrifuge/SRR7877884.classification.tsv Centrifuge output read classification TSV file
centrifuge/SRR7877884.report.tsv Centrifuge output report TSV file
centrifuge/SRR7877884.krona.html Centrifuge krona plot HTML file
gottcha2/SRR7877884.full.tsv GOTTCHA2 detail output TSV file
gottcha2/SRR7877884.tsv GOTTCHA2 output report TSV file
gottcha2/SRR7877884.krona.html GOTTCHA2 krona plot HTML file
kraken2/SRR7877884.classification.tsv Kraken2 output read classification TSV file
kraken2/SRR7877884.report.tsv Kraken2 output report TSV file
kraken2/SRR7877884.krona.html Kraken2 krona plot HTML file
======================================== ==============================================
.. list-table::
:header-rows: 1

* - Directory/File Name
- Description
* - SRR7877884.json
- ReadbasedAnalysis result JSON file
* - centrifuge/SRR7877884.classification.tsv
- Centrifuge output read classification TSV file
* - centrifuge/SRR7877884.report.tsv
- Centrifuge output report TSV file
* - centrifuge/SRR7877884.krona.html
- Centrifuge krona plot HTML file
* - gottcha2/SRR7877884.full.tsv
- GOTTCHA2 detail output TSV file
* - gottcha2/SRR7877884.tsv
- GOTTCHA2 output report TSV file
* - gottcha2/SRR7877884.krona.html
- GOTTCHA2 krona plot HTML file
* - kraken2/SRR7877884.classification.tsv
- Kraken2 output read classification TSV file
* - kraken2/SRR7877884.report.tsv
- Kraken2 output report TSV file
* - kraken2/SRR7877884.krona.html
- Kraken2 krona plot HTML file


Version History
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