petadimensionlab/docker_16s_pfastqdump repository overview

⁠Docker_16S

これは16Sの解析用のdockerイメージです。

⁠Docker_16S_pfastqdump⁠

これは16Sの解析用のdockerイメージです / This is a docker image for 16S analysis. (pfastqdump)

⁠Install & Run

docker pull petadimensionlab/docker_16s_pfastqdump

docker run -it -v /<Users_directory>/:/condir petadimensionlab/docker_16s_pfastqdump

⁠Usage

解析対象のデータを<Users_directory>に保存。 Save data to be analyzed in <Users_directory>.

cd vsearch_ubuntu/

python3 exec_make_configcsv.py <XXXXX> <yes or no>

python3 exec_DLSSRs.py <XXXXX>

python3 seq_exec_pfastqdump.py <XXXXX> <yes or no>

※ = Folder name of analyzed data ※ = PAIRED is yes , SINGLE is no

Continue analysis to petadimensionlab/docker_16s_vsearch⁠

⁠Docker_16S_vsearch⁠

これは16Sの解析用のdockerイメージです / This is a docker image for 16S analysis. (vsearch)

Continued from petadimensionlab/docker_16s_pfastqdump⁠.

⁠Install & Run

docker pull petadimensionlab/docker_16s_vsearch

docker run -it -v /<Users_directory>/:/condir petadimensionlab/docker_16s_vsearch

⁠Usage

解析対象のデータを<Users_directory>に保存。 Save data to be analyzed in <Users_directory>.

cd vsearch_ubuntu/

python3 exec_vsearch_full.py <XXXXX> <yes or no>

※ = Folder name of analyzed data ※ = PAIRED is yes , SINGLE is no

⁠Please select a reflist

exec_vsearch_full.py　 (line 63 to 68)

taxlist = { 'gg':gg97tax,'silva':silva_tax,'rdp':rdp_tax }
header = { 'gg':'gg','silva':'silva','rdp':'rdp' }

reflist = ['gg','silva','rdp']
ref = reflist[0]