SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

Updates for this release:

• Reworks the assign taxonomy command to use significantly less memory.
• The memory is now not dependent on the size of the alignment file.
• The LCA is now tree based instead of string based.
• It is possible to now do a confidence based LCA taxonomic profile

SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

• Fixed the LCA to properly remove spaces
• Added documentation and links to databases
• Started adding scripts for creating a custom database

SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

v1.0.6

Update setup.py

SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

Fixed a bug with relative abundance
Added some more proper testing

SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

Relative abundance added

SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

• Outputs the error from subcommand runs now. Formerly, it just displayed the errorcode.
• Fixed an error with aligners not taking in keyword arguments.

SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

Fixed the pipeline subcommand.

SHOGUN: Accurate, scalable metagenomic quantification with shallow shotgun sequencing

Adding some extra functionality with the fixing of issues #14, #15.

1. We can summarize KEGG tables into pathways
2. We can now summarize a KEGG table into modules and pathways given a KEGG table
3. You can now specify the taxacut parameter as a float on the command line (.5 <= taxacut < 1.0)
4. Contaminate filtering was sped up through BURST any mode

Release 1.0.0

This is release 1.0.0 of SHOGUN. SHOGUN is a commandline tool for taxonomic and functional profiling of short read next generation sequencing technology.

BugBase Release

This release is a snapshot that works as a shotgun taxonomic profiler for BugBase.

In the future, the APIs implemented for this release may change.