Bioinfo

Tools

Software	Topic
bwa	Mapping
centrifuge	Taxonomic classification of nucleotide sequences
kaiju	Taxonomic classification of amino acid sequences

Pipelines Snakemake

1. https://github.com/metagenome-atlas/atlas

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
19. http://merenlab.org/software/anvio/
20. http://www.bigsi.io
21. https://www.ebi.ac.uk/interpro/genomeproperties/#viewer
22. https://bioinf.shenwei.me/seqkit/
23. http://hannonlab.cshl.edu/fastx_toolkit/
24. https://deeptools.readthedocs.io/en/develop/index.html

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
3. sigma.js
4. https://visjs.org/ ==> http://subtiwiki.uni-goettingen.de/v3/interaction/view/A4C8719E06F774A6EB4D79757CC79CF89E453A54

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/