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Commits on Feb 25, 2017

• runs ccs protocol commandline for the pacbio data. input is file containing the list of all bas5 files (fullpath)

  aseetharam

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Commits on Feb 22, 2017

• renamed the files

  aseetharam

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• fixed path for the program

  aseetharam

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Commits on Feb 21, 2017

• added run gsnap script

  aseetharam

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Commits on Feb 16, 2017

• updated README file

  aseetharam

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• re-organized common analysis folder to keep only polished versions of run scripts

  aseetharam

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Commits on Feb 10, 2017

• modified busco to use the correct module on condo2017

  

  Arun Somwarpet-Seetharam - staff (sponsor severin)

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Commits on Feb 2, 2017

• Merge branch 'master' of github.com:ISUgenomics/common_analyses

  aseetharam

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• busco fix

  aseetharam

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Commits on Oct 24, 2016

• sort fasta by its name

  isugif

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Commits on Oct 14, 2016

• removed python from the front of the fasta_length.py command

  remkv6

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• Changed the picard module and variable to reflect current version

  remkv6

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Commits on Oct 12, 2016

• Merge branch 'master' of github.com:ISUgenomics/common_analyses

  remkv6

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• changed picard module and variable, and threads.

  remkv6

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Commits on Oct 6, 2016

• modifid CEGMA for condo

  aseetharam

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Commits on Sep 17, 2016

• added as ORG choice so that you don't have to modify the script, it can be run as runBUSCO_genome.sh genome.fasta metazoa

  isugif

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Commits on Sep 16, 2016

• needed fasta ending for polished output

  isugif

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• Merge branch 'master' of ssh://github.com/ISUgenomics/common_analyses

  isugif

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• added help and check to make sure you have at least 1 parameter

  isugif

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Commits on Sep 14, 2016

• updated module commands to accurately match the modules installed

  remkv6

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Commits on Sep 8, 2016

• fixed gatk path in gatk02 script

  aseetharam

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• updated picard_tools to picard and $PICARD to $PICARD_HOME

  remkv6

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• changed the file writing location for gatk 02 script

  aseetharam

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Commits on Jul 28, 2016

• changed ending to sh

  isugif

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• runBlasr.sub used primarily for comparing genomes either to themselves or to different versions of assemblies

  isugif

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• changed the help and the input to the fasta file

  isugif

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Commits on Jul 26, 2016

• Quiver analysis requires 2 steps for large datasets. this is my first rough draft of these scripts

  isugif

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Commits on Jun 6, 2016

• Added a plant version of runBUSCO script as it needs a different busco script

  aseetharam

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Commits on Jun 1, 2016

• test for slack integration

  remkv6

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Commits on May 31, 2016

• basic stats that can be gleaned from VCF file output from GATK

  isugif

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Commits on May 24, 2016

• added distruct.py to create Admixture plot

  isugif

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• runSTRUCTURE.sh is a script that will take a beagle imputed vcf file and generate a QMatrix file -- population structure file that is useful for MLM in TASSEL

  isugif

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• deleted example used to correct parameters

  isugif

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• moved beagle_PhaseImpute_VCF.sh to runBEAGLE_PhaseImpute.sh

  isugif

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• For beagle version 4 some parameters changed

  isugif

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