I have a new strain of Bacteria for which no reference genome is available at NCBI.
The strain is sequenced using Illumina and the paired-end reads were obtained. 

The pair-end reads were taken and subjected to De-novo assembly using CLC genomics workbench. Once the process of de-novo assembly was complete, the following results were obtained.

    Name	Consensus length	Total read count	Single reads	Reads in pairs	Average coverage
    contig_1_mapping	30575	24185	749	23436	116.3326574
    contig_2_mapping	4087	2703	111	2592	97.23562515
    contig_3_mapping	5764	3835	187	3648	97.76040944
    contig_4_mapping	7302	3488	152	3336	69.38989318
    contig_5_mapping	26530	16489	553	15936	91.15295891
    contig_6_mapping	5576	3883	119	3764	102.2159254
    contig_7_mapping	42110	33820	1166	32654	117.8527666

Then contig measurements were also obtained like `N75	N50	N25	Minimum	Maximum	Average	Count	Total`

And the following contigs details

        Name	Modified	Description	Size	Linear
    contig_1	Mon May  15:35:29 IST 2017	Average coverage: 116.33	30575	Linear
    contig_2	Mon May  15:35:29 IST 2017	Average coverage: 97.24	4087	Linear
    contig_3	Mon May  15:35:29 IST 2017	Average coverage: 97.76	5764	Linear
    contig_4	Mon May  15:35:29 IST 2017	Average coverage: 69.39	7302	Linear
    contig_5	Mon May  15:35:29 IST 2017	Average coverage: 91.15	26530	Linear
    contig_6	Mon May  15:35:29 IST 2017	Average coverage: 102.22	5576	Linear

Now how do I analyze and annotate these results which were obtained after doing de-novo assembly of the strain? Is there any NCBI tools to annotate these contigs?



Initial annotation:

   - prokka

   - [RAST][1]

Then you may wanto to use antiSMASH.

You may want to ckeck for contaminations with blobtools. 

Read [this][2] paper.


  [1]: http://rast.nmpdr.org/
  [2]: https://microbialinformaticsj.biomedcentral.com/articles/10.1186/2042-5783-3-2