BESST
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ksahlin
BESST - scaffolder for genomic assemblies
Hi, I am running BESST 2.2.8 in a python3 environment and get the following error: ``` Traceback (most recent call last): File "/home/ubuntu/anaconda3/bin/runBESST", line 4, in __import__('pkg_resources').run_script('BESST==2.2.8', 'runBESST') File "/home/ubuntu/anaconda3/lib/python3.6/site-packages/pkg_resources/__init__.py",...
Hello, I previous used a set of mate pair libraries to scaffold Allpath-LG scaffolds and was quite successful. Now I got a new assembly from nanopore contigs, and try to...
Hi, thank you for the tool. I am trying to run BESST after mapping the reads to the assembly with bwa, but it always ends up with the following error:...
Here is the patch for output as describe in issue #55 As mentionned it's a big changed. * check_kmer_overlap has been renamed compute_kmer_overlap as you suggested. I placed it outside...
This is my first time running `BESST`, have you ever seen this error before? ``` Warning: Orientations of library mappings not specified. Treating all libraries as fr mapped. If this...
Pls modify python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta --threads N to python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta /path/to/output --threads N Cost me a few core hours on each library, It started to...
I tested the new latest of besst. AGP output and GFF are still wrong. (my fault ! I'm the one who gave you the patch) I checked deeper the code...
Hi, in the std.output, there is this message showing up: ``` MathOverflow - too small stddev of library (12.7258430875bp) compared to the mean (465.185476795bp) - check distribution. 10.6473783941 0 0.666666666667...
A feature suggestion for the future is to have BESST output the scaffold graph in the GFA format, along with the Fasta and AGP files. It would be very nice...
Hi, the script "reads_to_ctg_map.py" fails at sam sort stage and give the following message" Convert SAM to BAM... Done. Time elapsed for SAM to BAM conversion: 0:03:52.958605 Sort BAM...Traceback (most...
