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Hi,
Unicycler is really a great pipeline with many useful tools. Although, I still have some doubts about its application and some steps, like the graph scaffolding and bridging:
1. Does Unicycler o…
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Canu is a very nice assembler. I have used it to de novo assemble four genomes. But, when i go to the fifth genome, the step of gfa for unitigging (unitigging/4-unitigger) is very very long time (more…
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Hi,
I am assembling a small region of a mammalian chromosome ( ~ 3.5Mb ) using PacBio CCS reads (3 passes + 0.900 accuracy) with Canu. I had a very high coverage ( > 100X for CCS reads) and the re…
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Hi,
This is an exciting tool - thanks for developing it. I am eager to get it up and running.
I installed and tried a simple test with 37X coverage of simulated lambda reads. All are 15000 bp long a…
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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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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 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…