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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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some questions of output files #11

Closed Axolotl233 closed 5 years ago

Axolotl233 commented 5 years ago

Hello, I m an ungreatute of lifescience institute, Lanzhou University. my name is Wenjie

I have tested your tools using some public data yesterday. It is amazing that the running speed of NextDenovo so fast, but after program processing, I have some questions confused

first is I do not know which is assembled most properest seqence, there have nine output directories of 02.cns_algin,please tell me how to selcet best and what are the differents among its.

secord is the folder named 03.ctg_graph is empty, whether I made some mistakes when I run program or input is improper. And what is means of 'graph' in thrid step, How is it different from 'assembly'?

my test data is ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR217/003/ERR2173373/ERR2173373.fastq.gz and my deploy file was uploaded in appendix.

all best. runcfg.txt

moold commented 5 years ago

Hi, Currently, we did not release the assembly module because of some reasons, you only can use NextDenovo to do error correction, and use the corrected seeds/reads as input for other assemblers, such as WTDBG. BTW, all files in 02.cns_align/01.get_cns.sh.work/get_cns*/cns.fasta are the corrected data, you need merge these files.