Reassembly after Binning

Question

[Tanker]

Hi everyone, I am new in Bioinformatics. Now I have some meta-genomics data of bacteria. After Assembling I want to practice binning. And I have seen somebody will reassembly after binning. This Reassembling can improve much more. But when I use Maxbin for binning, I will get some .fasta files. I am using spades or unicycler for assembling. These Assembling software cannot do assembling with .fasta files, only with .fastq file. Is there anything wrong? Should I still reassembly? When yes, is there any software, which can assembly with .fasta files? Thanks!

[andres.firrincieli]

an alternative to Jorg is the reassemble_bins module of metaWRAP

[Tanker]

I want to try it but metaWRAP is too big for me to download the database.

[andres.firrincieli]

You do not need to download any database except maybe checkM which is not that big

[Tanker]

yep, I think so. And now I have a new question. After binning I have used Checkm to assess the binning. And I have found that the completeness of bins is almost complementary (for example bin1-84% bin2-15%). May I merge this 2 bin*.fasta in one file?

[Zoonii]

Hey, where did you find the readme file for MaxBin? The links I'm finding to it aren't working.

[Tanker]

which readme file do you mean?

Answer 1

[Mensur Dlakic]

You are right about not being able to re-assemble from the .fasta files. Instead, you map the original .fastq reads to the bin sequences you are trying to re-assemble, and set those reads aside. Now you can assemble only from this subset using a true overlap assembler such as MIRA. It may be helpful to read this paper and try their software:

https://github.com/lmlui/Jorg

Even though their goal is to complete and circularize genomes which is not always possible, it is worth doing it even without circularization as long as you can improve the assembly statistics.

Also this paper may be helpful:

https://genome.cshlp.org/content/30/3/315.full

[Tanker]

Hello, I have tried the Jorg script but it can not run. Everytime when I try it, there is an Error: Writing log to file→No such file or directory(The "file" should be the *.log file.). Do you have this problem?

[Mensur Dlakic]

I don't have this problem. It is difficult to help you without seeing the whole command you are attempting to run. If you have a * character (an asterisk) somewhere in the command, that's probably the reason.

Also, you need a correct manifest_template.conf file to run MIRA. It is easiest to troubleshoot whether the installation is correct by running an example that comes with the program.

https://github.com/lmlui/Jorg/tree/master/Example

[Tanker]

Oh thank you! I have tried it. I must put all the files in the same directory. Even though I have written a right absolute path. But it is a pity that this reassembly script hat nothing changed. Maybe my data is not suitable. But thank you for your help!