Comments (2)
There are several parameters to compile it with threads
./configure --help
--with-threads compile with all threads
--with-thread-fr compile with two separate threads for Forward and Reverse sequence
--with-thread-aa compile with two separate threads for Assemble and Align steps
--with-thread-qc compile with threads for the query chunks
however, for multiple queries (multifasta for the first file) there is also a way to increase (inside the util.h file) the number of threads to process queries independently
util.h:#define MAX_QUERY_CHUNK_THREADS 4
PS : if you use yass on the web server "https://bioinfo.univ-lille.fr" , THEN when large files are provided by the user, the single threaded version is used : the reason is here to reduce the "memory footprint" (only one index is created at a time) so the program is more likely to terminate without "being terminated" 🤖
from yass.
... is slow for large fasta files ...
😐
- for full sensitivity with "rather small (weighted)" spaced seeds, yass will (always) be slow ...
- to cope with that, we now propose Minimally overlapping words seeds, or "Mow" 🚜✂️🌱 seeds
- they are less sensitive but an order of magnitude faster (as minimizers, but avoiding some of their artefacts 👍) : several are already provided in the https://bioinfo.univ-lille.fr/yass/seeds.txt file.
- they could be selected and used for the "Seed pattern:" in the bottom of https://bioinfo.univ-lille.fr/yass/yass.php but by now are not in the
[autoselect]
mode, only manual select enables them ...
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Related Issues (5)
- Manage dotplot windowsize HOT 1
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