RBGV Bioinformatics

(ERR): "Arabidopsis_simulated.plastome/seed/embplant_pt.index" does not exist or is not a Bowtie 2 index

11

Hi, I have installed using a manual method - git clone etc. But it seems to fail on test data building the bowtie index. Thanks, GetOrganelle v1.7.5.3 get_organelle_from_reads.py assembles organelle...

Add discussion - polyploid genomes

1

Hi, this is not really an issue - could I suggest the author adds a discussion page? There is much interest in assembling phased polyploids at the moment, especially in...

--n-hap 3 does not give three haploid genomes

1

I have a genome that BUSCO, genomescope and natural history suggest is triploid. When I use --n-hap 3 however, I only get hap1 and hap2 and the assembly is almost...

--dual-scaf

5

Hi, can you please describe the options '--dual-scaf' an d'--scaf-gap'. There is no description of it in the documentation. Is this for Hi-C scaffolding or ONT? Thanks, Theo

Please clarify scaffolding with HiC

2

Hi, I have a 0.9Gbp plant genome with HiFi and Hi-C data. HiFiasm has given me an assembly the correct size with 1000 contigs. Can you please clarify this paragraph...

smudgeplot.py hetkmers massive memory and walltime required

3

Hi, I have run this pipeline to generate the .dump file. However, smudgeplot.py hetkmers will not finish given 1200 GB of memory and 48 cpus: NCPUs Used: 48 CPU Time...

Hi, thanks for the very useful tool, pafCoordsDotPlotly.R. Would it be possible to colour reverse complement and forward alignments differently, e.g. red/blue. I can change the R code myself if...

I have manually installed EDTA and all it's dependencies (and their dependencies) they all appear to work normally. However: EDTA.pl --repeatmasker /g/data/nm31/bin/RepeatMasker --check_dependencies ######################################################## ##### Extensive de-novo TE Annotator (EDTA)...

"c" suffix on contigs

1

I have an assembly with a "c" suffix on one contig's name instead of the usual "l". What does this mean? Thanks.

See below. Running on Centos with boost: make augustus mkdir -p bin cd src && make make[1]: Entering directory '/g/data/nm31/bin/Augustus/src' g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3...