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Hey,
we have a lot of PE reads and want to assemble the cpdna from them using a seed from the **same species**. We get the above mentioned error with different seeds (ndhf, atpb). What can be the …
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I am new to bioinformatics. Recently, I tried to install FALCON-integrate on our centos linux server. The python version which I used is Python 2.7.12 :: Anaconda 4.2.0 (64-bit). The installation proc…
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I have:
- ONP data (about 1.1Gbp), 9.4 pores
- Genome size 7Mbp
- Most recent ABruijn version (pulled and compiled today)
- Many reads longer than 100kbp up to 700kbp max
I get the following er…
ghost updated
7 years ago
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Hi,
I am trying to do some SV detection and breakpoints mapping, but not being able to get it done for long, came across to your tool.
Can please tell me how can I install it in Linux and what are…
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Hi Chengxi,
Thank you for developing an easy-to-use hybrid assembler for large genomes.
When I run 'split_and_run_sparc.sh' script at the consensus step, both .m5 and .consensus.fasta files are…
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Hello,
I've noticed a significant slowdown with v1.5 versus v1.4 when running the exact command for assembling Pacbio corrected reads on a lsf cluster during the overlap jobs in 1-overlapper. The job…
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Hi,
I'm currently working on the assembly of endosymbiotic genomes and I would like to know if it is not problematic to working with linear genomes for NOVOPlasty. Do I've have to be careful with s…
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Hi,
I ran multiples instances of Pilon in parallel on different chunks of the genome like this:
```
java -Xmx450G -jar pilon-1.21.jar --outdir pilon --genome consensus.fasta --frags mapping.bam…
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Hi, I got a problem just like issus #259. But I didn't find the answer there.
RunPipeline command keeps failing, saying that project dir does not exist (even though the initPipeline completes and s…
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In relation to #184, I was testing the assembly benchmarking interface with
quast. I initially ran:
```
biobox
run \
assembler_benchmark \
bioboxes/quast \
--input-fasta=contigs.fa \
--outp…