Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update author list according to manuscript #124

Merged
merged 6 commits into from
Jan 30, 2020
Merged

Update author list according to manuscript #124

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
3a8663a
Merge pull request #1 from phac-nml/development
glabbe Jan 14, 2020
07a7cf8
Update README according to preprint v. 2020-01-10
glabbe Jan 14, 2020
6800e57
Update __init__.py
glabbe Jan 14, 2020
918d208
Update __init__.py
glabbe Jan 14, 2020
c13ca7f
Added genotype 2.2 to metadata file
glabbe Jan 29, 2020
eb9e4b9
Added genotype 2.2 to metadata table
glabbe Jan 29, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 5 additions & 5 deletions README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,9 +37,9 @@ If you find the ``biohansel`` tool useful, please cite as:

.. epigraph::

Rapid and robust genotyping of highly clonal bacterial pathogens using BioHansel, a SNP-based k-mer search pipeline.
Geneviève Labbé, Peter Kruczkiewicz, Philip Mabon, James Robertson, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo Taboada, Catherine Yoshida, Roger P. Johnson, Gary Van Domselaar and John H.E. Nash.
[Manuscript in preparation]
Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.
Geneviève Labbé, Peter Kruczkiewicz, Philip Mabon, James Robertson, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo Taboada, Catherine Yoshida, Kim Ziebell, Anil Nichani, Roger P. Johnson, Gary Van Domselaar and John H.E. Nash.
bioRxiv 2020.01.10.902056; doi: https://doi.org/10.1101/2020.01.10.902056


Read_The_Docs
Expand Down Expand Up @@ -130,7 +130,7 @@ If you run ``hansel -h``, you should see the following usage statement:

Subtype microbial genomes using SNV targeting k-mer subtyping schemes.
Includes schemes for Salmonella enterica spp. enterica serovar Heidelberg, Enteritidis, Typhi, and Typhimurium subtyping. Also includes a Mycobacterium tuberculosis scheme called 'tb_lineage'.
Developed by Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, David Son, Darian Hole, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.
Developed by Geneviève Labbé, Peter Kruczkiewicz, Philip Mabon, James Robertson, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo Taboada, Catherine Yoshida, Kim Ziebell, Anil Nichani, Roger P. Johnson, Gary Van Domselaar and John H.E. Nash.

positional arguments:
F Input genome FASTA/FASTQ files (can be Gzipped)
Expand Down Expand Up @@ -369,7 +369,7 @@ specific language governing permissions and limitations under the License.
Contact
=======

**Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca
**Gary van Domselaar**: gary.vandomselaar@canada.ca


.. _PyPI: https://pypi.org/project/bio-hansel/
Expand Down
2 changes: 1 addition & 1 deletion bio_hansel/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,5 @@
program_summary = 'Subtype microbial genomes using SNV targeting k-mer subtyping schemes.'
program_desc = program_summary + '''
Includes schemes for Salmonella enterica spp. enterica serovar Heidelberg, Enteritidis, Typhi, and Typhimurium subtyping. Also includes a Mycobacterium tuberculosis scheme called 'tb_lineage'.
Developed by Geneviève Labbé, Peter Kruczkiewicz, Philip Mabon, James Robertson, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo Taboada, Catherine Yoshida, Roger P. Johnson, Gary Van Domselaar and John H.E. Nash.
Developed by Geneviève Labbé, Peter Kruczkiewicz, Philip Mabon, James Robertson, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo Taboada, Catherine Yoshida, Kim Ziebell, Anil Nichani, Roger P. Johnson, Gary Van Domselaar and John H.E. Nash.
'''
3 changes: 2 additions & 1 deletion bio_hansel/data/tb_lineage/metadata.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ subtype Coll_et_al_genotype
1 1
1.1 1.1
2.1 2.1
2.2 2.2
3 3
4 4
4.1 4.1
Expand Down Expand Up @@ -58,4 +59,4 @@ subtype Coll_et_al_genotype
4.6.1.2 4.6.1.2
4.6.2 4.6.2
4.6.2.1 4.6.2.1
4.6.2.2 4.6.2.2
4.6.2.2 4.6.2.2