dnasko / baby_virome

Small virome analysis pipeline.

Bioinformatics Software Repo

Central repository for bioinformatic software and code

Collection of scripts for general sequecne analysis.

All production ready scripts are linked in the bin directory, by adding the "/Path/to/biobin/bin" to your PATH you should be all set.

Rev DJN 31May2017

baby_virome's Issues

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!

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?

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