-
@ksahlin
**Fix:** we had to comment this line in `main.cpp` to cancel parallelism:
`//#pragma omp parallel for num_threads(n_threads) shared(read_cnt, output_file, q_id) private(acc,seq_rc, que…
-
Strobealign currently uses [xxh64](https://github.com/ksahlin/strobealign/blob/8a0e047a451f4ff0ae74988f32695de0a0c80ea4/src/randstrobes.cpp#L38) to hash syncmers.
We could switch to a different, fa…
-
Hi, I am using the latest version 0.13, and when mapping reads against co-assembled contigs, no sam file is created. This message appears in the log file:
This is strobealign 0.13.0
Estimated rea…
-
I have used direct RNA-seq ONT long reads data. while running the rnabloom2, I got an error in the assembly step. I am not getting the reason behind it. could you help me out? I have pasted the comma…
-
Note to developer:
Using 32-bit hashes may reduce both vector and hash table size. For human, it is expected to reduce peak memory from 32Gb (64bit) down to around 20-24Gb
At the final hash valu…
-
### Background
Randstrobes is a method for linking two or more k-mers together into a seed that can be used for sequence mapping. I intend the below post to be a self-contained rough description of…
-
I ran rnabloom on several of my input files individually. out of my 10 samples, it did not produce any transcriptome file for 2 of them. Why is that? It finished running but there are no output files.…
-
Hello, I'm having problems with the program compiled through the source code running much slower than the version installed by bioconda.
### **Running environment:**
AMD EPYC 7T83, 64 * 2 cores (s…
-
Hello!
Here is the issue I am facing when trying to add a .fa file for a specific locus to db (locityper add).
[12:07:40 ESC[36mDEBUGESC[0m] locityper add -d HG03516/db/ -s HG03516/HG03516_MUC5…
-
Here is my to-do list for making strobealign work with references with more than $2^{32}$ strobemers. This will resolve #277 and #285.
- [x] Counters (unique strobemers, total no. of strobemers etc…