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Hyperlink DOIs to preferred resolver #1881

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Feb 13, 2019
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Hyperlink DOIs to preferred resolver #1881

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05fd61a
Hyperlink DOIs to preferred resolver
katrinleinweber Oct 27, 2018
ccbe7a8
Merge branch 'master' into resolve-DOIs-securely
standage Feb 13, 2019
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16 changes: 8 additions & 8 deletions CITATION
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Expand Up @@ -49,7 +49,7 @@ Software Citation
If you use the khmer software, you must cite:

Crusoe et al., The khmer software package: enabling efficient nucleotide
sequence analysis. 2015. http://dx.doi.org/10.12688/f1000research.6924.1
sequence analysis. 2015. https://doi.org/10.12688/f1000research.6924.1

.. code-block:: tex

Expand All @@ -76,7 +76,7 @@ If you use the khmer software, you must cite:
year = "2015",
month = "08",
publisher = "F1000",
url = "http://dx.doi.org/10.12688/f1000research.6924.1"
url = "https://doi.org/10.12688/f1000research.6924.1"
}

If you use any of our published scientific methods you should *also*
Expand All @@ -97,7 +97,7 @@ representation and partitioning algorithms described in:
Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT.
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7.
http://dx.doi.org/10.1073/pnas.1121464109.
https://doi.org/10.1073/pnas.1121464109.
PMID: 22847406

.. code-block:: tex
Expand Down Expand Up @@ -165,7 +165,7 @@ The :program:`script trim-low-abund.py` is described in:
Crossing the streams: a framework for streaming analysis of short DNA
sequencing reads
Zhang Q, Awad S, Brown CT
https://dx.doi.org/10.7287/peerj.preprints.890v1
https://doi.org/10.7287/peerj.preprints.890v1

.. code-block:: tex

Expand All @@ -175,7 +175,7 @@ The :program:`script trim-low-abund.py` is described in:
short DNA sequencing reads",
year = "2015",
eprint = "PeerJ Preprints 3:e1100",
url = "https://dx.doi.org/10.7287/peerj.preprints.890v1"
url = "https://doi.org/10.7287/peerj.preprints.890v1"
}

K-mer counting
Expand All @@ -188,7 +188,7 @@ counting described in:
These Are Not the K-mers You Are Looking For: Efficient Online K-mer
Counting Using a Probabilistic Data Structure
Zhang Q, Pell J, Canino-Koning R, Howe AC, Brown CT.
http://dx.doi.org/10.1371/journal.pone.0101271
https://doi.org/10.1371/journal.pone.0101271

.. code-block:: tex

Expand All @@ -202,7 +202,7 @@ counting described in:
year = "2014",
month = "07",
volume = "9",
url = "http://dx.doi.org/10.1371/journal.pone.0101271",
url = "https://doi.org/10.1371/journal.pone.0101271",
pages = "e101271",
abstract = "<p>K-mer abundance analysis is widely used for many purposes in
nucleotide sequence analysis, including data preprocessing for de novo
Expand Down Expand Up @@ -238,7 +238,7 @@ in:

SeqAn An efficient, generic C++ library for sequence analysis
Döring A, Weese D, Rausch T, Reinert K.
http://dx.doi.org/10.1186/1471-2105-9-11
https://doi.org/10.1186/1471-2105-9-11

.. code-block:: tex

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2 changes: 1 addition & 1 deletion doc/index.rst
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Expand Up @@ -48,7 +48,7 @@ shotgun sequencing data from genomes, transcriptomes, metagenomes, and
single cells. khmer can make *de novo* assemblies faster, and
sometimes better. khmer can also identify (and fix) problems with
shotgun data. You can read more about khmer in `our software paper
<https://dx.doi.org/10.12688/f1000research.6924.1>`__.
<https://doi.org/10.12688/f1000research.6924.1>`__.

khmer is free and open source software.

Expand Down
12 changes: 6 additions & 6 deletions khmer/khmer_args.py
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Expand Up @@ -62,16 +62,16 @@

ALGORITHMS = {
'software': 'MR Crusoe et al., '
'2015. http://dx.doi.org/10.12688/f1000research.6924.1',
'2015. https://doi.org/10.12688/f1000research.6924.1',
'diginorm': 'CT Brown et al., arXiv:1203.4802 [q-bio.GN]',
'streaming': 'Q Zhang, S Awad, CT Brown, '
'https://dx.doi.org/10.7287/peerj.preprints.890v1',
'graph': 'J Pell et al., http://dx.doi.org/10.1073/pnas.1121464109',
'https://doi.org/10.7287/peerj.preprints.890v1',
'graph': 'J Pell et al., https://doi.org/10.1073/pnas.1121464109',
'counting': 'Q Zhang et al., '
'http://dx.doi.org/10.1371/journal.pone.0101271',
'https://doi.org/10.1371/journal.pone.0101271',
'sweep': 'C Scott, MR Crusoe, and CT Brown, unpublished',
'SeqAn': 'A. Döring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11',
'hll': 'Irber and Brown. http://dx.doi.org/10.1101/056846'
'SeqAn': 'A. Döring et al. https://doi.org:80/10.1186/1471-2105-9-11',
'hll': 'Irber and Brown. https://doi.org/10.1101/056846'
}


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2 changes: 1 addition & 1 deletion sort-authors-list.py
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Expand Up @@ -70,7 +70,7 @@
year = "2015",
month = "08",
publisher = "F1000",
url = "http://dx.doi.org/10.12688/f1000research.6924.1"
url = "https://doi.org/10.12688/f1000research.6924.1"
}''')

doclist = u':Authors: '
Expand Down