Fernando Cruz

error extracting reads for scaffolding

2

Dear Aleksey, I have run the latest version on the grid (using slurm) to create the megarreads. After the create_megarreads job array finished I simply rerun ./assemble.sh and I obtained...

How to polish with long reads and short reads in Single-End mode

5

Hi, I have tried polishing an assembly with short-reads (HiC reads with -unpaired option in cfg) and long-reads (nextdenovo error corrected reads). But is taking longer than expected (before 5...

Dear Dominik, I've been using blobtools v1.1.1 for a couple of assembly projects and it worked pretty well at determining contaminant species. However, there is now a case where i...

Persistent "BLAST Database error" during Parallel all vs. all blast

3

Dear Andrew and Torsten, I am using Roary version 3.13.0, which I installed with conda. I've been computing the alignments with a subset of 24 E.coli samples. However I am...

segmentation fault building ctg_graph using NEXTDENOVO/2.4.0

1

**Describe the bug** I am running an assembly of 1.7G heterozygous genome (1.2% het rate) using a 2TB machine. The ONT data is 50x of the highest quality (used Filtlong...

empty alignments_sorted.txt file while generating .hic file

3

Dear Marbl Team, I've ran SALSA2 "successfully" on a genome assembly and scaffold N50 increased from 12Mb to 16Mb. In principle, everything looks good to me, except to what I...

Hi Maria, My understanding is that one the nucmer alignments are preprocessed with DotPrep.py, the visualization tool shows the longest unique alignments (based on their cumulative length) and the "Unique:...