Skip to content
Some interesting datasets and job description files for kameris
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
experiments
metadata
models
.test-settings.yml
.travis.yml
.yamllint.yml
LICENSE.txt Initial commit (docs) Jul 10, 2017
README.md
files.yml

README.md

kameris-experiments

Travis

This is a collection of datasets, job description files, and pre-trained models for use with Kameris.
By default, Kameris will attempt to find unknown dataset files and models from this repo, as described in files.yml.

Coming from a paper?

If you came here from:

"An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes"

See the experiments in the hiv1 folder as well as dengue, flu, hepatitis.

"Unravelling eukaryotic diversity with an alignment-free machine learning method"

See the experiments in the mmetsp and 1kplants folders.

Citing

If you use any of the datasets or experiments with names starting with hiv1, dengue, flu, or hepatitis in your research, please cite:

An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes
Stephen Solis-Reyes, Mariano Avino, Art Poon, Lila Kari
https://www.biorxiv.org/content/early/2018/07/05/362780

Experiments

Any of the following experiments can be easily run as follows:

  1. Visit https://github.com/stephensolis/kameris and follow the instructions to install Kameris.
  2. Create an empty folder and open a terminal in the folder.
  3. Create new folders data and output.
  4. Run kameris run-job https://raw.githubusercontent.com/stephensolis/kameris-experiments/master/experiments/[name of experiment].yml https://raw.githubusercontent.com/stephensolis/kameris/master/demo/settings.yml
Name Description
1kplants/1kplants Classify plant genomes into clade, order, and family, with different amounts of sampling per genome
dengue/ncbi-whole Classify dengue virus genomes by subtype
dna-types/mtdna-vs-plastid-vs-plasmid Classify whole organelle genomes by type: mitochondrial, plastid, and plasmid
dna-types/mtdna-vs-plastid Classify whole organelle genomes by type: mitochondrial and plastid
flu/ncbi-whole Classify influenza type A genomes by subtype, on different regions of the genome
genomes-nuclear/5kingdoms Classify whole nuclear genomes by 5 of the 6 kingdoms: animals, archaea, bacteria, fungi, and plants
genomes-nuclear/archaea Classify whole archaeal genomes into 3 phyla
genomes-nuclear/bacteria Classify whole bacterial genomes into 4 phyla or 5 proteobacterial classes
genomes-nuclear/fungi Classify whole fungal genomes into 3 phyla or subphyla
genomes-nuclear/plants Classify whole plant genomes into 2 clades
genomes-nuclear/vertebrates Classify whole vertebrate genomes into birds, fish, and mammals
hepatitis/hbv-whole Classify whole hepatitis B genomes by subtype
hepatitis/hcv-whole Classify whole hepatitis C genomes by subtype
hiv1/lanl-pol Classify whole HIV-1 pol genes by subtype
hiv1/lanl-reference-model Train the HIV-1 classifier on whole HIV-1 pol genes used in "An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes"
hiv1/lanl-whole Classify whole HIV-1 genomes by subtype
hiv1/real-vs-synthetic Classify natural vs. synthetic HIV-1 pol genes
hiv1/synthetic-pol Classify synthetic HIV-1 pol genes by subtype
human-haplogroups/human-haplogroups Classify whole human mitochondrial genomes by haplogroup
mmetsp/mmetsp-superphylum Classify marine microbial transcriptomes into superphylum, with different amounts of sampling per transcriptome
mmetsp/mmetsp Classify marine microbial transcriptomes into phylum, class, order, family, and genus, with different amounts of sampling per transcriptome
mtdna/amphibians Classify whole amphibian mitochondrial genomes into 3 orders
mtdna/fungi Classify whole fungal mitochondrial genomes into 3 phyla/subphyla
mtdna/insects-mammals-amphibians Classify whole animal mitochondrial genomes by class: insects, mammals, amphibians
mtdna/insects Classify whole insect mitochondrial genomes into 7 insect orders/superorders
mtdna/mammals Classify whole mammal mitochondrial genomes into 8 orders/superorders
mtdna/plants-animals-fungi-protists Classify whole eukaryote mitochondrial genomes by kingdom: plants, animals, fungi, protists
mtdna/plants Classify whole plant mitochondrial genomes into 2 clades
mtdna/primates Classify whole primate mitochondrial genomes into 2 suborders
mtdna/protists Classify whole protist mitochondrial genomes into 3 superphyla
mtdna/vertebrates Classify whole vertebrate mitochondrial genomes into amphibians, birds, fish, mammals, and reptiles
plasmids/bacteria Classify whole bacterial plasmid genomes into 4 phyla
plasmids/proteobacteria Classify whole protobacterial plasmid genomes into 3 classes
plastids/plants Classify whole plant plastid genomes into 5 clades
plastids/protists Classify whole protist plastid genomes into 3 superphyla
taxa/cpdna Classify whole choloroplast genomes from the same family or genus into genii or species
taxa/mtdna Classify whole mitochondrial genomes from the same family or genus into genii or species
viruses/dsDNA Classify whole dsDNA viral genomes by family
viruses/groups Classify whole viral genomes by group
viruses/retrotranscribing Classify whole retrotranscribing viral genomes by family
viruses/satellites Classify whole satellite viral genomes by family
viruses/ssDNA Classify whole ssDNA viral genomes by family
viruses/ssRNAnegative Classify whole (-)ssRNA viral genomes by family
viruses/ssRNApositive Classify whole (+)ssRNA viral genomes by family

Datasets

Name Description Retrieval instructions Retrieval date
1kplants Plant genome assemblies From the University of Alberta 1000 Plants (1kP) Initiative: metadata from http://www.onekp.com/samples/list.php and sequence data from http://www.onekp.com/public_data.html N/A (static dataset)
cpdna-all Whole chloroplast genomes From the NCBI Nucleotide database, https://www.ncbi.nlm.nih.gov/nucleotide/ with query "chloroplast"[Title] AND "complete"[Title] AND "genome"[Title] NOT "gene"[Title] NOT "contig"[Title] NOT "scaffold"[Title] NOT "cds"[Title] NOT "except"[Title] NOT "region"[Title] NOT "virus"[Title] NOT "plasmid"[Title] AND ("1000"[SLEN] : "999999999"[SLEN]). Results were manually reviewed and some sequences which were not whole genomes were removed. May 17, 2017
cpdna-taxa Whole chloroplast genomes, split into families/genii From the NCBI Nucleotide database, https://www.ncbi.nlm.nih.gov/nucleotide/ with query "<taxonomy ID>"[Organism:exp] AND "chloroplast"[Title] AND "complete"[Title] AND "genome"[Title] NOT "gene"[Title] NOT "contig"[Title] NOT "scaffold"[Title] NOT "cds"[Title] NOT "except"[Title] NOT "region"[Title] NOT "virus"[Title] NOT "plasmid"[Title] AND ("12000"[SLEN] : "99999999"[SLEN]) for every family with more than 50 sequence entries March 13, 2017
dengue-ncbi-whole Whole dengue virus genomes From the NCBI Virus Variation sequence database, https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/Database/nph-select.cgi?taxid=12637 with query options "Nucleotide", "Full-length sequences only", and "Collapse identical sequences" August 10, 2017
flu-ncbi Whole influenza genomes, split into genomic regions From the NCBI Virus Variation sequence database, https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=genomeset with query options "Genome sets: Complete only", and "Type: A, B" August 10, 2017
genomes-animals Whole assembled animal genomes From the NCBI Genome browser, https://www.ncbi.nlm.nih.gov/genome/browse/ with query options "Group: Animals", "Levels: Complete, Chromosome" June 15, 2017
genomes-archaea Whole assembled archaeal genomes From the NCBI Genome browser, https://www.ncbi.nlm.nih.gov/genome/browse/ with query options "Kingdom: Archaea", "Levels: Complete, Chromosome" June 24, 2017
genomes-bacteria Whole assembled bacterial genomes From the NCBI Genome browser, https://www.ncbi.nlm.nih.gov/genome/browse/ with query options "Kingdom: Bacteria", "Levels: Complete, Chromosome" June 25, 2017
genomes-fungi Whole assembled fungal genomes From the NCBI Genome browser, https://www.ncbi.nlm.nih.gov/genome/browse/ with query options "Group: Fungi", "Levels: Complete, Chromosome" June 24, 2017
genomes-plants Whole assembled plant genomes From the NCBI Genome browser, https://www.ncbi.nlm.nih.gov/genome/browse/ with query options "Group: Plants", "Levels: Complete, Chromosome" June 15, 2017
genomes-protists Whole assembled protist genomes From the NCBI Genome browser, https://www.ncbi.nlm.nih.gov/genome/browse/ with query options "Group: Protists", "Levels: Complete, Chromosome" June 15, 2017
hbv-ibcp-whole Whole hepatitis B genomes From the Hepatitis B Virus Database operated by the Institut de Biologie et Chimie des Proteines (IBCP), https://hbvdb.ibcp.fr/HBVdb/HBVdbDataset?seqtype=0 August 10, 2017
hcv-lanl-whole Whole hepatitis C genomes From the Los Alamos (LANL) sequence database, https://hcv.lanl.gov/components/sequence/HCV/search/searchi.html, with query options "Excluding recombinants", "Excluding 'no genotype'", "Genomic region: complete genome", and "Excluding problematic" August 10, 2017
hiv1-lanl-pol HIV-1 pol gene coding regions From the Los Alamos (LANL) sequence database, https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html with query options "Virus: HIV-1", "Genomic region: Pol CDS", "Excluding problematic" Retrieved May 18, 2017, site reported update May 6, 2017
hiv1-lanl-whole Whole HIV-1 genomes From the Los Alamos (LANL) sequence database, https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html with query options "Virus: HIV-1", "Genomic region: complete genome", "Excluding problematic" Retrieved May 18, 2017, site reported update May 6, 2017
hiv1-mixed-polfragments Natural HIV-1 pol gene fragments The curated testing dataset described in "An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes" See paper
hiv1-synthetic-polfragments Synthetically-generated HIV-1 pol gene fragments Described in "An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes" See paper
mmetsp Assembled marine eukaryote transcriptomes From the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): dataset information at https://www.imicrobe.us/#/projects/104 and data downloaded from ftp://ftp.imicrobe.us/projects/104/samples/ N/A (static dataset)
mtdna-all Whole mitochondrial genomes From the NCBI Nucleotide database, https://www.ncbi.nlm.nih.gov/nucleotide/ with query ("mitochondrial"[Title] OR "mitochondria"[Title] OR "mitochondrion"[Title]) AND "complete"[Title] AND "genome"[Title] NOT "gene"[Title] NOT "contig"[Title] NOT "scaffold"[Title] NOT "cds"[Title] NOT "except"[Title] NOT "region"[Title] NOT "virus"[Title] NOT "plasmid"[Title] AND ("1000"[SLEN] : "999999999"[SLEN]). Results were manually reviewed and some sequences which were not whole genomes were removed. May 17, 2017
mtdna-human-haplogroups Whole human mitochondrial genomes From the MITOMAP project (http://www.mitomap.org/MITOMAP/Mitobank), http://www.mitomap.org/foswiki/pub/MITOMAP/Mitobank/genbank_ids_2016June25.csv Database date June 25, 2016
mtdna-refseq Whole mitochondrial genomes From NCBI RefSeq release 81, ftp://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/ RefSeq release date March 6, 2017
mtdna-taxa Whole mitochondrial genomes, split into families/genii From the NCBI Nucleotide database, https://www.ncbi.nlm.nih.gov/nucleotide/ with query "<taxonomy ID>"[Organism:exp] AND ("mitochondrial"[Title] OR "mitochondria"[Title] OR "mitochondrion"[Title]) NOT "contig"[Title] NOT "scaffold"[Title] NOT "partial"[Title] NOT "cds"[Title] NOT "except"[Title] NOT "region"[Title] NOT "incomplete"[Title] AND ("12000"[SLEN] : "99999999"[SLEN]) for every family with more than 30 sequence entries. For family Hominidae, every Homo sapiens sequence except NC_012920.1 and NC_011137.1 was omitted. March 13, 2017
plasmids-all Whole plasmid genomes From the NCBI Nucleotide database, https://www.ncbi.nlm.nih.gov/nucleotide/ with query "plasmid"[Title] AND "complete"[Title] NOT "gene"[Title] NOT "contig"[Title] NOT "scaffold"[Title] NOT "cds"[Title] NOT "except"[Title] NOT "region"[Title] NOT "virus"[Title] NOT "coding"[Title] NOT "genes"[Title] NOT "pseudogene"[Title] NOT "protein"[Title] NOT "vector"[Title] NOT "operon"[Title] NOT "partial"[Title] NOT "transposon"[Title] NOT "rna"[Title] AND ("1000"[SLEN] : "999999999"[SLEN]). Results were manually reviewed and some sequences which were not whole genomes were removed. July 24, 2017
plasmids-refseq Whole plasmid genomes From NCBI RefSeq release 83, ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/ RefSeq release date July 21, 2017
plastids-refseq Whole plastid genomes From NCBI RefSeq release 82, ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plastid/ RefSeq release date May 15, 2017
viruses-all Whole viral genomes From the NCBI Nucleotide database, https://www.ncbi.nlm.nih.gov/nucleotide/ with query "txid10239"[Organism:exp] AND ("complete genome"[Title] OR "complete sequence"[Title]) NOT "miRNA"[Title] NOT "long terminal repeat"[Title] NOT "ltr"[Title] NOT "contig"[Title] NOT "spacer"[Title] NOT "pseudogene"[Title] NOT "genes"[Title] NOT "gene"[Title] NOT "segment"[Title] NOT "partial"[Title] NOT "cds"[Title] NOT "except"[Title] NOT "region"[Title] NOT "incomplete"[Title]. Results were manually reviewed and some sequences which were not whole genomes were removed. May 14, 2017
viruses-refseq Whole viral genomes From NCBI RefSeq release 83, ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ RefSeq release date July 21, 2017

Models

Name Description
hiv1-linearsvm HIV-1 subtypes classifier, trained using experiment hiv1/lanl-whole with settings k=6, include_recombinants=true, linear-svm classifier
hiv1-mlp HIV-1 subtypes classifier, trained using experiment hiv1/lanl-whole with settings k=6, include_recombinants=true, multilayer-perceptron classifier

License MIT CC0

The archives linked to in files.yml may contain copyrighted, proprietary, and/or confidential data. Use at your own risk.

The contents of this repository except for the metadata/ directory are licensed as follows:

The MIT License (MIT)

Copyright (c) 2017 Stephen

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

The contents of the metadata/ directory are licensed as follows:

CC0 1.0 Universal

Statement of Purpose

The laws of most jurisdictions throughout the world automatically confer
exclusive Copyright and Related Rights (defined below) upon the creator and
subsequent owner(s) (each and all, an "owner") of an original work of
authorship and/or a database (each, a "Work").

Certain owners wish to permanently relinquish those rights to a Work for the
purpose of contributing to a commons of creative, cultural and scientific
works ("Commons") that the public can reliably and without fear of later
claims of infringement build upon, modify, incorporate in other works, reuse
and redistribute as freely as possible in any form whatsoever and for any
purposes, including without limitation commercial purposes. These owners may
contribute to the Commons to promote the ideal of a free culture and the
further production of creative, cultural and scientific works, or to gain
reputation or greater distribution for their Work in part through the use and
efforts of others.

For these and/or other purposes and motivations, and without any expectation
of additional consideration or compensation, the person associating CC0 with a
Work (the "Affirmer"), to the extent that he or she is an owner of Copyright
and Related Rights in the Work, voluntarily elects to apply CC0 to the Work
and publicly distribute the Work under its terms, with knowledge of his or her
Copyright and Related Rights in the Work and the meaning and intended legal
effect of CC0 on those rights.

1. Copyright and Related Rights. A Work made available under CC0 may be
protected by copyright and related or neighboring rights ("Copyright and
Related Rights"). Copyright and Related Rights include, but are not limited
to, the following:

  i. the right to reproduce, adapt, distribute, perform, display, communicate,
  and translate a Work;

  ii. moral rights retained by the original author(s) and/or performer(s);

  iii. publicity and privacy rights pertaining to a person's image or likeness
  depicted in a Work;

  iv. rights protecting against unfair competition in regards to a Work,
  subject to the limitations in paragraph 4(a), below;

  v. rights protecting the extraction, dissemination, use and reuse of data in
  a Work;

  vi. database rights (such as those arising under Directive 96/9/EC of the
  European Parliament and of the Council of 11 March 1996 on the legal
  protection of databases, and under any national implementation thereof,
  including any amended or successor version of such directive); and

  vii. other similar, equivalent or corresponding rights throughout the world
  based on applicable law or treaty, and any national implementations thereof.

2. Waiver. To the greatest extent permitted by, but not in contravention of,
applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and
unconditionally waives, abandons, and surrenders all of Affirmer's Copyright
and Related Rights and associated claims and causes of action, whether now
known or unknown (including existing as well as future claims and causes of
action), in the Work (i) in all territories worldwide, (ii) for the maximum
duration provided by applicable law or treaty (including future time
extensions), (iii) in any current or future medium and for any number of
copies, and (iv) for any purpose whatsoever, including without limitation
commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes
the Waiver for the benefit of each member of the public at large and to the
detriment of Affirmer's heirs and successors, fully intending that such Waiver
shall not be subject to revocation, rescission, cancellation, termination, or
any other legal or equitable action to disrupt the quiet enjoyment of the Work
by the public as contemplated by Affirmer's express Statement of Purpose.

3. Public License Fallback. Should any part of the Waiver for any reason be
judged legally invalid or ineffective under applicable law, then the Waiver
shall be preserved to the maximum extent permitted taking into account
Affirmer's express Statement of Purpose. In addition, to the extent the Waiver
is so judged Affirmer hereby grants to each affected person a royalty-free,
non transferable, non sublicensable, non exclusive, irrevocable and
unconditional license to exercise Affirmer's Copyright and Related Rights in
the Work (i) in all territories worldwide, (ii) for the maximum duration
provided by applicable law or treaty (including future time extensions), (iii)
in any current or future medium and for any number of copies, and (iv) for any
purpose whatsoever, including without limitation commercial, advertising or
promotional purposes (the "License"). The License shall be deemed effective as
of the date CC0 was applied by Affirmer to the Work. Should any part of the
License for any reason be judged legally invalid or ineffective under
applicable law, such partial invalidity or ineffectiveness shall not
invalidate the remainder of the License, and in such case Affirmer hereby
affirms that he or she will not (i) exercise any of his or her remaining
Copyright and Related Rights in the Work or (ii) assert any associated claims
and causes of action with respect to the Work, in either case contrary to
Affirmer's express Statement of Purpose.

4. Limitations and Disclaimers.

  a. No trademark or patent rights held by Affirmer are waived, abandoned,
  surrendered, licensed or otherwise affected by this document.

  b. Affirmer offers the Work as-is and makes no representations or warranties
  of any kind concerning the Work, express, implied, statutory or otherwise,
  including without limitation warranties of title, merchantability, fitness
  for a particular purpose, non infringement, or the absence of latent or
  other defects, accuracy, or the present or absence of errors, whether or not
  discoverable, all to the greatest extent permissible under applicable law.

  c. Affirmer disclaims responsibility for clearing rights of other persons
  that may apply to the Work or any use thereof, including without limitation
  any person's Copyright and Related Rights in the Work. Further, Affirmer
  disclaims responsibility for obtaining any necessary consents, permissions
  or other rights required for any use of the Work.

  d. Affirmer understands and acknowledges that Creative Commons is not a
  party to this document and has no duty or obligation with respect to this
  CC0 or use of the Work.
You can’t perform that action at this time.