[bioman1]

Lol..I didn't it is a prank script..

I have another sequence using a whole-genome shotgun strategy of illumina paired-end reads, but this sequence from
another variety belong the same crop. (say for eg. I have WGS sequence of Apple (variety 1 and variety2), If I have
low contig N50 by de novo genome assembling variety 1. Can I combine and variety 1 and variety 2 paired-end reads
and do de novo genome assembly?

I have additional transcriptome sequences from different tissue of variety 1, how can I use this sequence
for genome assembly?

[WhatsOEver]

I have another sequence using a whole-genome shotgun strategy of illumina paired-end reads, but this sequence from
another variety belong the same crop. (say for eg. I have WGS sequence of Apple (variety 1 and variety2), If I have
low contig N50 by de novo genome assembling variety 1. Can I combine and variety 1 and variety 2 paired-end reads
and do de novo genome assembly?

In principle, I would say yes. The human reference genome is also just a mixture of genomes - although, this is not directly comparable to your case, of course...
The success mainly depends on how close your different varieties are. But give it a try - there is nothing to loose
Btw: You never answered my question whether the genome of a relative crop species has been sequenced so far. A reference-guided assembly can improve your own assembly quite significantly (if you are lucky).

I have additional transcriptome sequences from different tissue of variety 1, how can I use this sequence
for genome assembly?

Just do a de novo assembly on these and use them as contigs together with your existing contigs. There are some tools that are elongating your contigs by looking for overlaps with other contigs in your dataset. BBmerge is one of them for example (http://seqanswers.com/forums/showthread.php?t=43906)

[bioman1]

@WhatsoEver. Thanks for your suggestion.

1.My crop is non-model. I don't know the close relative crop species.
2. I have only WGS sequence with one paired end for each variety with same insert size around 300 bp. (variety 1 & 2- one paired-end file (PE1 & 2). There is no additional libraries with different insert size.
3. Does automated genome size estimation of kmer genie & SGA preqc will be accurate method for estimation or I should trust on manual 17-mer jellyfish estimation?.

[WhatsOEver]

1.My crop is non-model. I don't know the close relative crop species.
2. I have only WGS sequence with one paired end for each variety with same insert size around 300 bp. (variety 1 & 2- one paired-end file (PE1 & 2). There is no additional libraries with different insert size.
3. Does automated genome size estimation of kmer genie & SGA preqc will be accurate method for estimation or I should trust on manual 17-mer jellyfish estimation?.

1. If you don't have the time/money to do a re-sequencing of your genome, but still want to come close to something like a partially complete genome, you have to try some things. That you don't know the close relative, doesn't tell me that there is no relatively close species available which has been sequenced...
2. see (1) You simply have to try it.
3a. Kmer genie doesn't give you a genome size estimation, but gives you an estimation of the best Kmer to choose for assembly. I think it's working fine and is definitely a better approach then just guessing.
3b. I have never heard of the program before, but from the description it sounds like something you should try.