-
I have an application where I need to count pairs of k-mers separated by a fixed distance. This is almost identical to K-mer counting where K=2k, the "only" change should be in the scanning step where…
-
I ran spades.py on my reads to have a plant genome assemby which has an estimated size of 600M. I am providng a memory of 998G but it was stuck at subclustering hamming graph for 2 days. I have Nanopo…
-
Hi,
Not sure if it's a spades specific issue but I was running the same command on two linux computer due to memory issue and oberved a huge difference of speed despite having more memory/cores on th…
-
Hi,
I am trying to get the taxonomy of several contigs present in a multi-fasta file, but I'm having some issues with the `easy-taxonomy` command, as it is has not completed the assignment of about …
-
**#This following is the params.txt**
Command line: ./../SPAdes-3.13.1-Linux/bin/spades.py --careful -t 20 --pe1-1 /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC…
-
Hello,
I am getting an error while indexing of the BAM files. I have installed the tool using conda. So the kallisto version is at 0.44 as mentioned. Below is STDOUT
```
Results stored in: stra…
-
### Description of bug
When I run `metaspades.py` via a conda environment, the process will run but no contig files are created. I seem to get all the intermediate files. I was able to assemble suc…
-
I am not sure about below details can you please confirm,
Data structure and Sorting Algo: Enhanced suffix arrays/Counting using the lcp-interval tree
Approach: In-memory
The limit of k-size : Ar…
-
Hello! Thanks for your helpful tool!
I am trying to assemble long-read sequencing data with short-read polishing. My long read data (nanopore direct RNA sequencing) are from the animals under 25 de…
-
Hi,
I do not see any output files. It looks like it ran but in the end it says "killed"......
```
./ProSampler.unix -i /home/premsubramaniam/Desktop/TFEA_output/LNCAP_WT01_peaks.fasta -o out_
…