Releases: knights-lab/UTree
UTree 2.0: Rank-Free Edition
Combined static 64-bit Linux/WindowsWSL release for rank-free edition of UTree 2.0.
This version does not enforce a set number of taxonomic levels (before it enforced 8). This unlocks the potential to use it for all sorts of fun hierarchical interpolations!
Note that the default build binary is now in a cluster build configuration. It is not intended for use on systems with less than 96GB of RAM. For a RAM-light build, use the 'small' version instead (but this takes a lot more time to build huge DBs). As before, SSE4 is required.
To cite:
Al-Ghalith, Gabriel and Dan Knights. Faster and lower-memory metagenomic profiling with UTree. DOI: 10.5281/zenodo.998252
UTree 2.0 SigNature Edition: SHOGUN release
Combined static release for SHOGUN 1.0
v2.0 (build):
- Faster DB building
- Signature-based (micro-alignment) compression
- User-controllable "Compression" parameter during DB build
- Higher levels give smaller databases at the expense of sensitivity
- Now technically feasible to perform full long-read metagenomic shotgun DB search on your phone/tablet (couple with minION?)
Since v1.5 (same search binary):
- totally rewritten search_gg for robustness and (better) fault tolerance
- Vast (order-of-magnitude) speedup with 8+ cores
Approx. ~20 million queries per minute with RC and full Aufbau interpolation on our server - Configurable Aufbau Proportion (compatible w/BURST's --taxacut/--bc) for confidence (compile w/-D TAXACUT=8 or whatever; default is 4, old mode closer to 2-ish behavior)
- Multi-level confidence score reporting: support value summaries and taxonomic per-level reports
- Prints out version string, progress when it runs
To cite:
Al-Ghalith, Gabriel and Dan Knights. Faster and lower-memory metagenomic profiling with UTree. DOI: 10.5281/zenodo.998252
UTree v2.0 SigNature Edition
- Faster DB building
- Signature-based (micro-alignment) compression
- User-controllable "Compression" parameter during DB build
- Higher levels give smaller databases at the expense of sensitivity
- Now technically feasible to perform full long-read metagenomic shotgun DB search on your phone/tablet (couple with minION?)
UTREE v1.5a (GG Linux release)
New v1.5:
- totally rewritten search_gg for robustness and (better) fault tolerance
- Vast (order-of-magnitude) speedup with 8+ cores
Approx. ~20 million queries per minute with RC and full Aufbau interpolation on our server - Configurable Aufbau Proportion (compatible w/BURST's --taxacut/--bc) for confidence (compile w/-D TAXACUT=8 or whatever; default is 4, old mode closer to 2-ish behavior)
- Multi-level confidence score reporting: support value summaries and taxonomic per-level reports
- Prints out version string, progress when it runs
UTREE v1.2b (GG Linux release)
Latest linux release for build, search
Also works on Windows 10 Creators or newer (WSL)
UTree v1.2 Release
Now includes more commandline options and output features. Also includes 16- and 64-mer editions.
Also, GG editions may be added later if there is demand.
