How do I analyze and annotate the results of a Bacterial De novo assembly ?

Question

[Paul]

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?

[Joe]

What do you mean by 'analyse'? What do you want to know? h.mon's suggestions for annotation are probably the best 2 annotators currently.

Answer 1

[h.mon]

Initial annotation:

• prokka

• RAST

Then you may wanto to use antiSMASH.

You may want to ckeck for contaminations with blobtools.

Read this paper.

Answer 2

[nora]

for annotation you can use artemis