Difference between revisions of "Bioinfo"

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=Tools=
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= Tools =
 
  
  
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
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! Header text !! Header text !! Header text
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!
 +
!Header text!!Header text!!Header text
 
|-
 
|-
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| Example || Example || Example
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|BWA
 +
|[test link]||Example||Example
 
|-
 
|-
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| Example || Example || Example
+
|
 +
|Example||Example||Example
 
|-
 
|-
−
| Example || Example || Example
+
|
 +
|Example||Example||Example
 
|}
 
|}
  
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== BWA ==
+
==BWA==
  
 
[[BWA Usage]]
 
[[BWA Usage]]
  
−
== Kaiju ==
+
==Kaiju==
  
 
[[Kaiju Usage]]
 
[[Kaiju Usage]]
  
−
== Centrifuge ==
+
==Centrifuge==
  
 
[[Centrifuge Usage]]
 
[[Centrifuge Usage]]
  
−
= Links =
+
=Links=
  
−
# https://github.com/snayfach/MIDAS
+
#https://github.com/snayfach/MIDAS
−
# https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
+
#https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
−
# http://calcul.math.cnrs.fr/IMG/pdf/presentation.pdf
+
#http://calcul.math.cnrs.fr/IMG/pdf/presentation.pdf
−
# https://github.com/gjospin/PhyloSift
+
#https://github.com/gjospin/PhyloSift
−
# http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
+
#http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
−
# https://github.com/JoseBlanca/seq_crumbs
+
#https://github.com/JoseBlanca/seq_crumbs
−
# https://github.com/soedinglab/MMseqs2/wiki#install-static-linux-version
+
#https://github.com/soedinglab/MMseqs2/wiki#install-static-linux-version
−
# https://github.com/SaierLaboratory/BioVx/blob/master/scripts/gblast3.py
+
#https://github.com/SaierLaboratory/BioVx/blob/master/scripts/gblast3.py
−
# https://ccb.jhu.edu/software/bracken/
+
#https://ccb.jhu.edu/software/bracken/
−
# http://motu-tool.org/  
+
#http://motu-tool.org/
−
# https://www.ebi.ac.uk/metagenomics/
+
#https://www.ebi.ac.uk/metagenomics/
−
# https://www.nature.com/articles/d41586-018-07196-1
+
#https://www.nature.com/articles/d41586-018-07196-1
−
# https://www.taxonomer.com/
+
#https://www.taxonomer.com/
−
# http://segatalab.cibio.unitn.it/tools/
+
#http://segatalab.cibio.unitn.it/tools/
−
# https://academic.oup.com/nar/article/45/2/e7/2953304
+
#https://academic.oup.com/nar/article/45/2/e7/2953304
−
# https://www.nature.com/articles/nmeth.3802
+
#https://www.nature.com/articles/nmeth.3802
−
# https://research.bioinformatics.udel.edu/peptidematch/index.jsp
+
#https://research.bioinformatics.udel.edu/peptidematch/index.jsp
−
# http://lab.dessimoz.org/blog/2018/10/01/human-plant-orthologs-p2
+
#http://lab.dessimoz.org/blog/2018/10/01/human-plant-orthologs-p2
  
−
= Biblio =
+
=Biblio=
  
−
# https://www.nature.com/articles/s41586-018-0703-0.epdf?shared_access_token=gm4GZr3P2ZZxDN8RGNy7LdRgN0jAjWel9jnR3ZoTv0N9OWpzII7VEgb2rgQ968D8MuuDkP3J2YZRratQgCRBTWXIBHcUKnD0HqETn9DHIBBPy5h4d7-POMKMRzGuhjJ8D3O4jLPrj4JrH7tG6gNQ6GQV77d_1eo568aMvymB-GU%3D
+
#https://www.nature.com/articles/s41586-018-0703-0.epdf?shared_access_token=gm4GZr3P2ZZxDN8RGNy7LdRgN0jAjWel9jnR3ZoTv0N9OWpzII7VEgb2rgQ968D8MuuDkP3J2YZRratQgCRBTWXIBHcUKnD0HqETn9DHIBBPy5h4d7-POMKMRzGuhjJ8D3O4jLPrj4JrH7tG6gNQ6GQV77d_1eo568aMvymB-GU%3D
−
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090853/
+
#https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090853/
−
# https://watermark.silverchair.com/msy123.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAkgwggJEBgkqhkiG9w0BBwagggI1MIICMQIBADCCAioGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMHUixy6gkLUA3-pjLAgEQgIIB-y5PdqIXTXk8tHL2nlaGIkx8nd-e6zdeifITsMs_WhG6Ri-iq0a_7w4lbB8DB8sTYrQefo0r0t5kda2AcRpaljP6V9pazbnx0nI_8qYqSUHlwazmGiXp2d01On_dz0CnsWnU3_9lBG8V8BWqxFLxtoDGcpDEi7QuEGOfNqXtvFLIzjDktbIORSiGSbpfqHo43UXby9IIDgnh8QmKoDm6zegZ_l2xVsPFJX1g_TvJToF9e0ORWuexNBGE5yMpKIN26aVse4BeS5lnrW-TXkLAvLh7eKNSMYznL4FK4gklCDFvDf6dAESrCgIEjbmBRGR5R6zTh3Ldw5PRHdLSquUXZ3sxqAGYZkFq2msd86fxaBqwE5UhJQHbNDsR1UD6CdfI7Dr12rCaqJgWyEHjwU9d-TNvZpu6buSBESQAgOjwEB7fWZc2MdyijGfD8dPYdkbsHYwiCjVxiSXXlIVehpRo8rNz9T9k7z38WYSLOjnELMRDl1NTerZyVRz2ixGQzLkXz7D0_iGvfgh6LIlvtYnfAQZmX1hBDfaxTjMbQwVJjvT8DS3dmXgYoc2J8sdEpi2dUwb6gt3XUbxbskvaYfDXo0JeQTPq5wftD54Iwp74VdYw5gHssdtFkbLLsh83ao2dtNDnlu0Uc2QB7gQ_TYRBmYPB3UzhkuTgaHOy0g
+
#https://watermark.silverchair.com/msy123.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAkgwggJEBgkqhkiG9w0BBwagggI1MIICMQIBADCCAioGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMHUixy6gkLUA3-pjLAgEQgIIB-y5PdqIXTXk8tHL2nlaGIkx8nd-e6zdeifITsMs_WhG6Ri-iq0a_7w4lbB8DB8sTYrQefo0r0t5kda2AcRpaljP6V9pazbnx0nI_8qYqSUHlwazmGiXp2d01On_dz0CnsWnU3_9lBG8V8BWqxFLxtoDGcpDEi7QuEGOfNqXtvFLIzjDktbIORSiGSbpfqHo43UXby9IIDgnh8QmKoDm6zegZ_l2xVsPFJX1g_TvJToF9e0ORWuexNBGE5yMpKIN26aVse4BeS5lnrW-TXkLAvLh7eKNSMYznL4FK4gklCDFvDf6dAESrCgIEjbmBRGR5R6zTh3Ldw5PRHdLSquUXZ3sxqAGYZkFq2msd86fxaBqwE5UhJQHbNDsR1UD6CdfI7Dr12rCaqJgWyEHjwU9d-TNvZpu6buSBESQAgOjwEB7fWZc2MdyijGfD8dPYdkbsHYwiCjVxiSXXlIVehpRo8rNz9T9k7z38WYSLOjnELMRDl1NTerZyVRz2ixGQzLkXz7D0_iGvfgh6LIlvtYnfAQZmX1hBDfaxTjMbQwVJjvT8DS3dmXgYoc2J8sdEpi2dUwb6gt3XUbxbskvaYfDXo0JeQTPq5wftD54Iwp74VdYw5gHssdtFkbLLsh83ao2dtNDnlu0Uc2QB7gQ_TYRBmYPB3UzhkuTgaHOy0g
−
# https://research.pasteur.fr/fr/project/population-genomics/
+
#https://research.pasteur.fr/fr/project/population-genomics/
−
# https://medium.com/@infoecho/the-end-of-a-chapter-a-memoir-on-bioinformatics-development-work-for-single-molecule-sequencing-19455c288280
+
#https://medium.com/@infoecho/the-end-of-a-chapter-a-memoir-on-bioinformatics-development-work-for-single-molecule-sequencing-19455c288280
−
# https://watermark.silverchair.com/bbw020.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlowggJWBgkqhkiG9w0BBwagggJHMIICQwIBADCCAjwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMq2CbkYjDYcR3lshgAgEQgIICDcfmCZSqsrJPkLxOgW2ftW4xru0PuqsKrx4TG05vnF9dedAd9P8Ya8xn3gjY7dsC1XtnUoxhj0J9x9gXI3-N0KI1oVSxy5BpUX6f40iJS9L5tBSv2FAAK108r983tECXELKnATZj1HQYtz9RCkasj3tsA5QxQULDHcgj195vsn6fGulC3StrzNnbEu4oZuk6e2LAEQJbSYHE8UsDw2yngo0s80FaHyWhduJynK_NsdIwt2aVXV2HB7BZG0uTYYQU0-R00wX75wjDg5hrdW3lsYIvq87XlmyKAkug_vCHyh0rOURVZXZXRlqd5uxj4zgb1jgMU5ue18RWxe00Rw_ZoHnaVIUSbM5E7xLEUA6hFS2Gqmoe1_j5Gq_b21dWVi3exT2TpIrzc2GpZbw3a5IegaaI9yTEICauJ21UhzPXNzCmR9aLqc45kDj5Kahhc2pV3sNMANyReqMuQc9SREa7BVA58L-FVEVOVYzREG837X29bRzEIPK1SMtE-n2f4WXNOdDK--M7jumgKJubztly_cNZfnC_hfGYBRNmBf4dWDXuFE50RfWdpnVkYMtXvWGrk5rJ6tpwvR490vhVKCWoaWLFm00R9yI9sTiReSUapvGaxyw77Uq1rdoDcjAgcETYlXUpvqC7Q2GsAXtJiVi7NMo-XZz-sDcY9hOfElIMiQCEk7CwWfQZ6X6aMEakhg
+
#https://watermark.silverchair.com/bbw020.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlowggJWBgkqhkiG9w0BBwagggJHMIICQwIBADCCAjwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMq2CbkYjDYcR3lshgAgEQgIICDcfmCZSqsrJPkLxOgW2ftW4xru0PuqsKrx4TG05vnF9dedAd9P8Ya8xn3gjY7dsC1XtnUoxhj0J9x9gXI3-N0KI1oVSxy5BpUX6f40iJS9L5tBSv2FAAK108r983tECXELKnATZj1HQYtz9RCkasj3tsA5QxQULDHcgj195vsn6fGulC3StrzNnbEu4oZuk6e2LAEQJbSYHE8UsDw2yngo0s80FaHyWhduJynK_NsdIwt2aVXV2HB7BZG0uTYYQU0-R00wX75wjDg5hrdW3lsYIvq87XlmyKAkug_vCHyh0rOURVZXZXRlqd5uxj4zgb1jgMU5ue18RWxe00Rw_ZoHnaVIUSbM5E7xLEUA6hFS2Gqmoe1_j5Gq_b21dWVi3exT2TpIrzc2GpZbw3a5IegaaI9yTEICauJ21UhzPXNzCmR9aLqc45kDj5Kahhc2pV3sNMANyReqMuQc9SREa7BVA58L-FVEVOVYzREG837X29bRzEIPK1SMtE-n2f4WXNOdDK--M7jumgKJubztly_cNZfnC_hfGYBRNmBf4dWDXuFE50RfWdpnVkYMtXvWGrk5rJ6tpwvR490vhVKCWoaWLFm00R9yI9sTiReSUapvGaxyw77Uq1rdoDcjAgcETYlXUpvqC7Q2GsAXtJiVi7NMo-XZz-sDcY9hOfElIMiQCEk7CwWfQZ6X6aMEakhg
  
−
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165453/
+
#https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165453/
  
−
= Estimation du génome sur la base des kmer =
+
=Estimation du génome sur la base des kmer=
  
−
# http://kmergenie.bx.psu.edu/
+
#http://kmergenie.bx.psu.edu/
−
# https://khmer-recipes.readthedocs.io/en/latest/003-estimate-genome-size/index.html
+
#https://khmer-recipes.readthedocs.io/en/latest/003-estimate-genome-size/index.html
−
# https://khmer-recipes.readthedocs.io/en/latest/005-estimate-total-genome-size/
+
#https://khmer-recipes.readthedocs.io/en/latest/005-estimate-total-genome-size/
−
# https://khmer-recipes.readthedocs.io/en/latest/
+
#https://khmer-recipes.readthedocs.io/en/latest/
−
# http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html
+
#http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html
  
−
= Meteganomic: taxonomic assignation =
+
=Meteganomic: taxonomic assignation=
  
−
# http://porecamp.github.io/2017/metagenomics.html
+
#http://porecamp.github.io/2017/metagenomics.html
−
# https://ccb.jhu.edu/software/centrifuge/manual.shtml
+
#https://ccb.jhu.edu/software/centrifuge/manual.shtml
  
−
= Networks =
+
=Networks=
  
−
# youtube network
+
#youtube network
  
−
# http://www.yasiv.com/youtube#?Search%3Fq=write%20in%20c&q=N'to%20-%20La%20Cl%C3%A9%20Des%20Champs
+
#http://www.yasiv.com/youtube#?Search%3Fq=write%20in%20c&q=N'to%20-%20La%20Cl%C3%A9%20Des%20Champs
−
# https://github.com/anvaka/VivaGraphJS
+
#https://github.com/anvaka/VivaGraphJS
  
−
= maps =
+
=maps=
  
−
# word density maps:
+
#word density maps:
  
−
= Installation de ScanIndel (+BLAT) =
+
=Installation de ScanIndel (+BLAT)=
  
 
- https://github.com/cauyrd/ScanIndel
 
- https://github.com/cauyrd/ScanIndel
 
- via conda
 
- via conda
 
- donwloder executables manquant: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/
 
- donwloder executables manquant: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

Revision as of 22:28, 29 January 2019

Tools

Header text Header text Header text
BWA [test link] Example Example
Example Example Example
Example Example Example

BWA

BWA Usage

Kaiju

Kaiju Usage

Centrifuge

Centrifuge Usage

Links

  1. https://github.com/snayfach/MIDAS
  2. https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
  3. http://calcul.math.cnrs.fr/IMG/pdf/presentation.pdf
  4. https://github.com/gjospin/PhyloSift
  5. http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
  6. https://github.com/JoseBlanca/seq_crumbs
  7. https://github.com/soedinglab/MMseqs2/wiki#install-static-linux-version
  8. https://github.com/SaierLaboratory/BioVx/blob/master/scripts/gblast3.py
  9. https://ccb.jhu.edu/software/bracken/
  10. http://motu-tool.org/
  11. https://www.ebi.ac.uk/metagenomics/
  12. https://www.nature.com/articles/d41586-018-07196-1
  13. https://www.taxonomer.com/
  14. http://segatalab.cibio.unitn.it/tools/
  15. https://academic.oup.com/nar/article/45/2/e7/2953304
  16. https://www.nature.com/articles/nmeth.3802
  17. https://research.bioinformatics.udel.edu/peptidematch/index.jsp
  18. http://lab.dessimoz.org/blog/2018/10/01/human-plant-orthologs-p2

Biblio

  1. https://www.nature.com/articles/s41586-018-0703-0.epdf?shared_access_token=gm4GZr3P2ZZxDN8RGNy7LdRgN0jAjWel9jnR3ZoTv0N9OWpzII7VEgb2rgQ968D8MuuDkP3J2YZRratQgCRBTWXIBHcUKnD0HqETn9DHIBBPy5h4d7-POMKMRzGuhjJ8D3O4jLPrj4JrH7tG6gNQ6GQV77d_1eo568aMvymB-GU%3D
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090853/
  3. https://watermark.silverchair.com/msy123.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAkgwggJEBgkqhkiG9w0BBwagggI1MIICMQIBADCCAioGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMHUixy6gkLUA3-pjLAgEQgIIB-y5PdqIXTXk8tHL2nlaGIkx8nd-e6zdeifITsMs_WhG6Ri-iq0a_7w4lbB8DB8sTYrQefo0r0t5kda2AcRpaljP6V9pazbnx0nI_8qYqSUHlwazmGiXp2d01On_dz0CnsWnU3_9lBG8V8BWqxFLxtoDGcpDEi7QuEGOfNqXtvFLIzjDktbIORSiGSbpfqHo43UXby9IIDgnh8QmKoDm6zegZ_l2xVsPFJX1g_TvJToF9e0ORWuexNBGE5yMpKIN26aVse4BeS5lnrW-TXkLAvLh7eKNSMYznL4FK4gklCDFvDf6dAESrCgIEjbmBRGR5R6zTh3Ldw5PRHdLSquUXZ3sxqAGYZkFq2msd86fxaBqwE5UhJQHbNDsR1UD6CdfI7Dr12rCaqJgWyEHjwU9d-TNvZpu6buSBESQAgOjwEB7fWZc2MdyijGfD8dPYdkbsHYwiCjVxiSXXlIVehpRo8rNz9T9k7z38WYSLOjnELMRDl1NTerZyVRz2ixGQzLkXz7D0_iGvfgh6LIlvtYnfAQZmX1hBDfaxTjMbQwVJjvT8DS3dmXgYoc2J8sdEpi2dUwb6gt3XUbxbskvaYfDXo0JeQTPq5wftD54Iwp74VdYw5gHssdtFkbLLsh83ao2dtNDnlu0Uc2QB7gQ_TYRBmYPB3UzhkuTgaHOy0g
  4. https://research.pasteur.fr/fr/project/population-genomics/
  5. https://medium.com/@infoecho/the-end-of-a-chapter-a-memoir-on-bioinformatics-development-work-for-single-molecule-sequencing-19455c288280
  6. https://watermark.silverchair.com/bbw020.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlowggJWBgkqhkiG9w0BBwagggJHMIICQwIBADCCAjwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMq2CbkYjDYcR3lshgAgEQgIICDcfmCZSqsrJPkLxOgW2ftW4xru0PuqsKrx4TG05vnF9dedAd9P8Ya8xn3gjY7dsC1XtnUoxhj0J9x9gXI3-N0KI1oVSxy5BpUX6f40iJS9L5tBSv2FAAK108r983tECXELKnATZj1HQYtz9RCkasj3tsA5QxQULDHcgj195vsn6fGulC3StrzNnbEu4oZuk6e2LAEQJbSYHE8UsDw2yngo0s80FaHyWhduJynK_NsdIwt2aVXV2HB7BZG0uTYYQU0-R00wX75wjDg5hrdW3lsYIvq87XlmyKAkug_vCHyh0rOURVZXZXRlqd5uxj4zgb1jgMU5ue18RWxe00Rw_ZoHnaVIUSbM5E7xLEUA6hFS2Gqmoe1_j5Gq_b21dWVi3exT2TpIrzc2GpZbw3a5IegaaI9yTEICauJ21UhzPXNzCmR9aLqc45kDj5Kahhc2pV3sNMANyReqMuQc9SREa7BVA58L-FVEVOVYzREG837X29bRzEIPK1SMtE-n2f4WXNOdDK--M7jumgKJubztly_cNZfnC_hfGYBRNmBf4dWDXuFE50RfWdpnVkYMtXvWGrk5rJ6tpwvR490vhVKCWoaWLFm00R9yI9sTiReSUapvGaxyw77Uq1rdoDcjAgcETYlXUpvqC7Q2GsAXtJiVi7NMo-XZz-sDcY9hOfElIMiQCEk7CwWfQZ6X6aMEakhg
  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165453/

Estimation du génome sur la base des kmer

  1. http://kmergenie.bx.psu.edu/
  2. https://khmer-recipes.readthedocs.io/en/latest/003-estimate-genome-size/index.html
  3. https://khmer-recipes.readthedocs.io/en/latest/005-estimate-total-genome-size/
  4. https://khmer-recipes.readthedocs.io/en/latest/
  5. http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html

Meteganomic: taxonomic assignation

  1. http://porecamp.github.io/2017/metagenomics.html
  2. https://ccb.jhu.edu/software/centrifuge/manual.shtml

Networks

  1. youtube network
  1. http://www.yasiv.com/youtube#?Search%3Fq=write%20in%20c&q=N'to%20-%20La%20Cl%C3%A9%20Des%20Champs
  2. https://github.com/anvaka/VivaGraphJS

maps

  1. word density maps:

Installation de ScanIndel (+BLAT)

- https://github.com/cauyrd/ScanIndel - via conda - donwloder executables manquant: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

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