Number of contigs is too big

Question

[Bioinfo]

Hello . i hope you're doing fine i have question please , i have Illumina Miseq data for bacteria set , when i performed assembly i got too many conting in results ( 7165 ) what may be the causes of this results and how ca i improve the results of the assembly ?

Thank you

[GenoMax]

Please provide additional information about the expected size of the genome. Size/type of the dataset and/or methods used for the assembly. This is important so you would not get suggestions of things to try that you may have already done.

[Bioinfo]

the expected genome size is 19146100 and the total length that I found is 6534152((-65.87%)) , and here's the command I used

shovill --outdir Assembly_Miseq_Default --R1 R1_001.fastq –R2 _R2_001.fastq

[GenoMax]

How many reads went into this assembly and what was their length? In other words what was the total size (base pairs) or data you used for this assembly.

[Bioinfo]

2842610 reads in the file 1 and 2842610 in the file 2 and their length is 250

[GenoMax]

So you seem to have ~75x coverage in terms of bases sequenced (if my calculation is right). In theory this should be enough coverage to get a reasonably good assembly.

There is always the possibility that a) your libraries are not that good (have a lot of technical duplication, over-amplification) b) you are not doing the assemblies right or have used the correct aligner that would work. Since those possibilities are hard to assess to in a forum like this you are going to have to work on those yourself.

If there are related genomes available in GenBank you can try to do a reference assisted genome assembly to see if that helps.

[Ram]

i performed assembly

What software did you use? What were the parameters you passed? Is there a log file? Were there any warnings or errors? How do you know the software was run accurately?

i got too many contigs in results

How do you know they are too many contigs? How many did you expect? How are these contigs different in composition/length from the ones you expected?

Once you look for the answers to the above questions, you'll probably find a good lead to the solution, if not the solution itself.

[Bioinfo]

Hello

I used shovill for the assembly and I performed this command

shovill --outdir wDil_Assembly_Miseq_Default --R1 R1_001.fastq –R2  _R2_001.fastq

and also I tried specific kmer

shovill  --kmer 127--outdir wDil_Assembly_Miseq_Default --R1 R1_001.fastq –R2  _R2_001.fastq

I performed assembly of Hiseq data of the same bacteria and I found better results (1664 contigs ) that what makes me think that the result of Miseq data is abnormal