lotts/glassgo repository overview

The Docker Image contains the software package GLASSgo based on the GitHub located sources (https://github.com/lotts/GLASSgo⁠). GLASSgo is also available on a web-server "http://rna.informatik.uni-freiburg.de/GLASSgo/Input.jsp⁠" and the web-server version does also provide an interactive graphical taxonomic representation. Please cite us if your are using GLASSgo for your work (https://doi.org/10.3389/fgene.2018.00124⁠).

⁠Usage:

1. Get Image
   • docker pull lotts/glassgo
2. Get positive ACC-Lists from Zenodo
   • https://zenodo.org/record/1320180⁠
3. Get the latest NCBI nt-database
   • ftp://ftp.ncbi.nlm.nih.gov/blast/db/
4. Create a GLASSgo instance and mount all needed volumes
   • docker run -v $PWD/BLAST_NT:/BLAST_NT -v $PWD/ACC_LISTS:/ACC_LISTS -v $PWD/SRNA_INPUT:/SRNA_INPUT -it -d <image_id> /bin/bash
5. Execute GLASSgo
   • docker exec -it <container_id> ./GLASSgo.py -d /BLAST_NT/nt -i /SRNA_INPUT/<my_sRNA.fasta> -g /ACC_LISTS/<my_prefered_acc_list>

⁠Most important GLASSgo parameters:

-i    input_file (single sRNA sequence in FASTA format)
-o    output_file (optional, default: stdout)
-e    E-Value (default: 1)
-p    lower limit for pairwise identity (default: 52)
-g    path to ACC-List (optional)  (default: global search)
-d    path to NCBI nt-database
-t    number of threads for performing the BLAST search (default: 1)
-u    upstream region (default: 0)