dnasko / baby_virome Goto Github PK
View Code? Open in Web Editor NEWSmall virome analysis pipeline.
License: GNU General Public License v3.0
baby_virome's Issues
Connecting to ftp.theseed.org (ftp.theseed.org)|192.5.200.3|:21... failed: Connection timed out.
Hello,
When I try to run the './scripts/create_database.sh' script to download the SEED database, the connection could not be established.
Is there any alternative for this?
Contig abundance info with assemblers other than spades
I have assemblies using Megahit and other non-spades assemblers. It would be sweet if I could use them in the pipeline!
Functional Script
With the new uniref update the function_assignment.pl per_query output doesnt work. Looks like this:
NODE_1_length_65404_cov_16.5831_646_1_1 17.6945438216094
NODE_1_length_65404_cov_16.5831_646_1_1 17.6945438216094
NODE_1_length_65404_cov_16.5831_646_1_1 17.6945438216094
NODE_1_length_65404_cov_16.5831_646_1_1 17.6945438216094
NODE_1_length_65404_cov_16.5831_646_1_1 17.6945438216094
NODE_1_length_65404_cov_16.5831_1484_660_2 16.8737841024269
NODE_1_length_65404_cov_16.5831_1951_1496_3 22.854549511651
NODE_1_length_65404_cov_16.5831_1951_1496_3 22.854549511651
NODE_1_length_65404_cov_16.5831_1951_1496_3 22.854549511651
NODE_1_length_65404_cov_16.5831_2888_1944_4 19.1865853712293
NODE_1_length_65404_cov_16.5831_2888_1944_4 19.1865853712293
NODE_1_length_65404_cov_16.5831_2888_1944_4 19.1865853712293
NODE_1_length_65404_cov_16.5831_2888_1944_4 19.1865853712293
NODE_1_length_65404_cov_16.5831_2888_1944_4 19.1865853712293
NODE_1_length_65404_cov_16.5831_3333_2899_5 16.543755169369 GO:0030430
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