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Issue assembling plant genome with NECAT #47
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Hi, The folders 4-fsa, 5-align_contigs and 6-bridge_contigs need to be renamed or deleted before running the command |
Hi, |
Hi @LeoVincenzi |
Some raw reads are broken into multiple corrected reads in the error correction step. The unbroken raw reads are used to bridge the contigs, so the assembler can output the longer N50. |
Hi,
I'm working on a plant genome and I'm trying to assemble it with NECAT, but the final assembly I obtain is really inconsistent.
The expected genome size is 1.2 Gbp and I'm working with Oxford Nanopore reads. The starting data for the assembly are reported in the following table:
The obtained results are the following:
The command I run was
/opt/NECAT/Linux-amd64/bin/necat.pl assemble config.txt
and the config file was compiled as it follows:
I would like to understand why the assembly obtained is so poor and how can I improve it. Maybe the parameters used for this dataset are inadequate?
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