Metagenomics
Modules included in this section
HUMAnN2
- Authors
Menachem Sklarz
- Affiliation
Bioinformatics core facility
- Organization
National Institute of Biotechnology in the Negev, Ben Gurion University.
Note
This module was developed as part of a study led by Dr. Jacob Moran Gilad
A module for running HUMAnN2
:
Requires
fastq files, either forward or single:
sample_data[<sample>]["fastq.F"]
sample_data[<sample>]["fastq.S"]
Output
Puts the
HUMAnN2
output files in:self.sample_data[sample]["HUMAnN2.genefamilies"]
(Also inHUMAnN2.genefamilies.RPK
)self.sample_data[sample]["HUMAnN2.pathabundance"]
(Also inHUMAnN2.pathabundance.RPK
)self.sample_data[sample]["HUMAnN2.pathcoverage"]
If
humann2_renorm_table
block is set in params, puts the normalized tables in:self.sample_data[sample]["HUMAnN2.genefamilies"]
(Also inHUMAnN2.genefamilies.<units>
, where<units>
is the value passed to--units
)self.sample_data[sample]["HUMAnN2.pathabundance"]
(Also inHUMAnN2.pathabundance.<units>
, where<units>
is the value passed to--units
)
If
humann2_join_tables
block is set in params, puts the joined tables in:self.sample_data["project_data"]["HUMAnN2.genefamilies"]
self.sample_data["project_data"]["HUMAnN2.pathabundance"]
self.sample_data["project_data"]["HUMAnN2.pathcoverage"]
Note
If both humann2_renorm_table
and humann2_join_tables
blocks exist in params, humann2_join_tables
will work on the normalized tables produced by humann2_renorm_table
! To join the non-normalized tables, do not normalize the tables by not including a humann2_renorm_table
block.
Parameters that can be set
Parameter |
Values |
Comments |
---|---|---|
humann2_join_tables |
Block containing |
|
humann2_renorm_table |
Block containing |
|
protein-database |
uniref50|uniref90 |
Protein database used for analysis. |
Warning
The protein-database
parameter records the protein database being used: uniref50 or uniref90. It is not used by this module but is required by the downstream module, HUMAnN2_further_processing
. If you do not include it, you will not be able to add a HUMAnN2_further_processing
instance for downstream analysis.
Lines for parameter file
HUMAnN2_uniref50_hardtrimmed_reads:
module: HUMAnN2
base: Trim_Galore
script_path: '{Vars.Programs_path.humann2}'
setenv: PERL5LIB="" mpa_dir=$CONDA_PREFIX/bin
qsub_params:
-pe: shared 30
protein-database: uniref50
redirects:
--gap-fill: 'on'
--input-format: fastq
--minpath: 'on'
--nucleotide-database: '{Vars.databases.humann2.chocophlan}'
--protein-database: '{Vars.databases.humann2.uniref50}'
--threads: '30'
humann2_join_tables:
path: humann2_join_tables
humann2_renorm_table:
path: humann2_renorm_table
redirects:
--units: cpm
References
kraken
- Authors
Menachem Sklarz
- Affiliation
Bioinformatics core facility
- Organization
National Institute of Biotechnology in the Negev, Ben Gurion University.
Note
This module was developed as part of a study led by Dr. Jacob Moran Gilad
A module for running kraken
:
Note that kraken
executable must be in a folder together with kraken-translate
and kraken-report
. This is the default for kraken
installation.
Pass the full path to the kraken
executable in script_path
.
Merging of sample kraken reports in done with krona. See the section on Parameters that can be set.
You can follow this module with the kraken-biom
module to create a biom table from the reports.
Requires
fastq files, either paired end or single:
sample_data[<sample>]["fastq.F"]
sample_data[<sample>]["fastq.R"]
sample_data[<sample>]["fastq.S"]
Output
Puts the
kraken
output files in:self.sample_data[<sample>]["raw_classification"]
self.sample_data[<sample>]["classification"]
self.sample_data[<sample>]["kraken.report"]
If
ktImportTaxonomy_path
parameter was passed, puts the krona reports inself.sample_data["project_data"]["krona"]
Parameters that can be set
Parameter |
Values |
Comments |
---|---|---|
ktImportTaxonomy_path |
Path to ktImportTaxonomy. You can additional |
Lines for parameter file
kraken1:
module: kraken
base: trim1
script_path: {Vars.paths.kraken}
qsub_params:
-pe: shared 20
ktImportTaxonomy_path: /path/to/ktImportTaxonomy -u http://krona.sourceforge.net
redirects:
--db: /path/to/kraken_std_db
--preload:
--quick:
--threads: 20
References
Wood, D.E. and Salzberg, S.L., 2014. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome biology, 15(3), p.R46.
kraken_biom
- Authors
Menachem Sklarz
- Affiliation
Bioinformatics core facility
- Organization
National Institute of Biotechnology in the Negev, Ben Gurion University.
Note
This module was developed as part of a study led by Dr. Jacob Moran Gilad
A module for running kraken-biom
(https://github.com/smdabdoub/kraken-biom)
Requires
Kraken reports:
sample_data[<sample>]["kraken.report"]
Output
Puts the resulting biom output files in:
self.sample_data["project_data"]["kraken.biom"]
self.sample_data["project_data"]["biom_table"]
self.sample_data["project_data"]["biom_table_tsv"]
(ifskip_tsv
is not set)
Parameters that can be set
Parameter |
Values |
Comments |
---|---|---|
skip_tsv |
Set if you do not want to convert the report into tsv format. |
|
skip_summary |
Set if you do not want to create a summary of the report. |
|
biom_path |
/path/to/biom |
The path to biom. This is required for conversion to tsv and for producing the summary |
Lines for parameter file
kraken_biom1:
module: kraken_biom
base: kraken1
script_path: '{Vars.paths.kraken_biom}'
# skip_tsv:
biom_path: '{Vars.paths.biom}'
redirects:
--max: D
--min: S
--gzip:
References
metaphlan2
- Authors
Menachem Sklarz
- Affiliation
Bioinformatics core facility
- Organization
National Institute of Biotechnology in the Negev, Ben Gurion University.
Note
This module was developed as part of a study led by Dr. Jacob Moran Gilad
A module for running metaphlan2
:
Requires
fastq files, either paired end or single:
sample_data[<sample>]["fastq.F"]
sample_data[<sample>]["fastq.R"]
sample_data[<sample>]["fastq.S"]
Output
Puts the
metaphlan2
output files in:self.sample_data[<sample>]["raw_classification"]
If
If
ktImportText_path
parameter was passed, puts the krona reports inself.sample_data["project_data"]["krona"]
If
merge_metaphlan_tables
was passed, puts the merged reports inself.sample_data["project_data"]["merged_metaphlan2"]
If ‘–biom’ is set in
redirects
, the biom table is put in:self.sample_data[<sample>]["biom_table"]
If ‘–bowtie2out’ is set in
redirects
, the SAM file is put in:self.sample_data[<sample>]["sam"]
If ‘metaphlan2krona_path’ is set:
self.sample_data[<sample>]["classification"]
Parameters that can be set
Parameter |
Values |
Comments |
---|---|---|
ktImportText_path |
Path to ktImportText. |
|
merge_metaphlan_tables |
Path to merge_metaphlan_tables.py. If not specified, will derive it from the location of |
|
metaphlan2krona_path |
Path to metaphlan2krona.py |
Lines for parameter file
metph1:
module: metaphlan2
base: trim1
script_path: {Vars.paths.metaphlan2}
ktImportText_path: /path/to/ktImportText
merge_metaphlan_tables:
metaphlan2krona_path: /path/to/metaphlan2krona.py
redirects:
--biom:
--bowtie2_exe: /path/to/bowtie2
--bowtie2db: /path/to/database
--bowtie2out:
--input_type: fastq
--mdelim: ';'
--mpa_pkl: /path/to/mpa_v20_m200.pkl
References
Truong, D.T., Franzosa, E.A., Tickle, T.L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C. and Segata, N., 2015. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nature methods, 12(10), pp.902-903.
centrifuge
- Authors
Menachem Sklarz
- Affiliation
Bioinformatics core facility
- Organization
National Institute of Biotechnology in the Negev, Ben Gurion University.
Note
This module was developed as part of a study led by Dr. Jacob Moran Gilad
A module for running centrifuge
:
Pass the full path to the centrifuge
executable in script_path
.
Merging of sample centrifuge reports in done with krona. See the section on Parameters that can be set.
Requires
fastq files, either paired end or single:
sample_data[<sample>]["fastq.F"]
sample_data[<sample>]["fastq.R"]
sample_data[<sample>]["fastq.S"]
Output
Puts the
centrifuge
output files in:self.sample_data[<sample>]["raw_classification"]
self.sample_data[<sample>]["classification"]
self.sample_data[<sample>]["classification_report"]
If
ktImportTaxonomy_path
parameter was passed, puts the krona reports inself.sample_data["project_data"]["krona"]
Parameters that can be set
Parameter |
Values |
Comments |
---|---|---|
ktImportTaxonomy_path |
Path to ktImportTaxonomy. You can additional |
Lines for parameter file
Centrifuge:
module: centrifuge
base: trim1
script_path: {Vars.paths.centrifuge}
qsub_params:
-pe: shared 20
ktImportTaxonomy_path: /path/to/ktImportTaxonomy -u http://krona.sourceforge.net
redirects:
--db: /path/to/centrifuge_db
--preload:
--quick:
--threads: 20
References
Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome research, 26(12), 1721-1729.