Dear All,
I would like to prepare statistical report from my fastq data.
I was responsible for project with bacterial genome:
1. 1st step - it was de novo assembly (after that I choose possible reference sequence, and...)
2. 2nd step - it was resequencing project (I choose bowtie2 alignment)
After that I used also basys platform for automated annotation.

Now, I have some questions:
A. Is there any possibility to prepare some statistic about sequencing project with ugene platform and included scripts? I mean length distribution, GC-content (I think I saw that), average phred score, and base-quality distribution?


B. non matched sequence - as I write, I used chosen sequence as a reference one, after de novo sequencing I have seen some contigs in which I recognised some plasmids sequences, after resequencing step I think I lost this data (or I do not know where to find this reads...) Can you suggest something in that case? I mean de novo assembly using data which do not match to the "refseq"


Sorry for such many questions, but I really enjoy your platform as a easy to use for people with not to big knowledge about unix...

Regards
L.

Dear Olga,

my goal?
A) main task - to identify and obtain sequence of bacterial DNA
I decided to use de novo as a first step (for free in illumina base space platform, but I have got to much reads to use free spades tool there, that's why i was looking for system like yours), but it gives me only partial information, but helpful in looking for possible reference sequence ( I have checked it manually using BLAST)
After that I choose "refseq" and do resequencing... (very nice coverage - near 1000x, no gaps...., but also i do not know how to sort reads which do not match to my refseq).
B) minor task - plasmids... or another add-ons

For resequencing I used your platform and bowtie2, and obtained consensus I uploaded to basys platform (now I got annotated sequence),
Do I do something wrong? what is a typical pipeline for this kind of task?
Now I am using clc tool, I have similar but different consensus sequence obtained from the same reads and the same refseq, using unmatched reads I was able to perform de novo sequencing and I have some huge fragments of DNA (different set of plasmids, still analyse it)

Another project - unknown bacteriophages sequencing project - I think I need spades for that...
but still have a problem with my data... I used new release of UGENE but it does not change anything. Tomorrow I will have my IT specialist, I am not familiar with unix system, he will help me with command line (I know, you have write my almost everything ). Tomorrow I will try to use Win version of UGENE, and I will see what I have after using clc tool...

Sorry for my silence, but I had long break from work, today is my second day.

Regards
L.