SOAPdenovo

[Jingjing Jin]

Dear all,

I am interested in the SOAPdenovo software.

For my dataset, the length for the pair end is about 100bp, the number is about 500 million for one end.

After I run the SOAPdenovo on it, I want to use other scaffold algorithm on the contig file.

However, when use the bowtie trying to align the read to the contig file, I find the results is like this:

# reads processed: 406265561
# reads with at least one reported alignment: 76432204 (18.81%)
# reads that failed to align: 329833357 (81.19%)
Reported 76432204 paired-end alignments to 1 output stream(s)

From the results, it seems that only 18.81% of reads align to the contig file.


Do you think it is reasonable? The contig file is generated from my raw reads file, why only 18.81% reads align to them?

Then, I have checked the log file of SOAPdenovo, I also find the similar results for the scaffold step:

75464691 link to masked contigs, 0 links on a single scaff
Insert size 300: 84425805 links input
Cutoff for number of pairs to make a reliable connection: 3
6454014 weak connects removed (there were 17922228 active cnnects))
392 circles removed
variance for insert size 30
a remove transitive lag, 84213 connections removed
a remove transitive lag, 0 connections removed
Picked 2864031 subgraphs,14080 have conflicting connections,2758081 have significant overlapping, 2659 eligible
maskRepeat: 1012341 contigs masked from 1225101 puzzles
a remove transitive lag, 18461 connections removed
a remove transitive lag, 0 connections removed
Picked 164027 subgraphs,2261 have conflicting connections,153297 have significant overlapping, 2 eligible
non-strict linearization
Picked 149646 subgraphs,4801 have conflicting connections,134374 have significant overlapping, 2 eligible
Masked 71233 contigs, 0 puzzle left
Freezing is done....
232 contigs recovered
all links loaded
time spent on creating scaffolds 644s

Hence, can you give me some suggestions about whether the result is reasonable?

And if I want to use other scaffold algorithm, should I filter the short contig first?

Thanks!

Jingjing

[Ruibang Luo]

Very possible that your bowtie parameters are incorrect.

rb

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[Jingjing Jin]

The parameter I use for the bowtie is like this:

bowtie -S -p 2 --threads 16 --chunkmbs 1024 /SOAPdenovo_31_new/bowtie_index/oil_palm -1 DNA1.fastq_filtered -2 DNA2.fastq_filtered SOAP_contig_bowtie.sam

Do you think it is wrong?

Thanks!

JIngjing

________________________________________
From: bgi-...@googlegroups.com [bgi-...@googlegroups.com] On Behalf Of Ruibang Luo [luoru...@genomics.org.cn]
Sent: Wednesday, June 13, 2012 9:57 PM
To: bgi-...@googlegroups.com
Subject: Re: [BGI-SOAP:459] SOAPdenovo

[刘兵行]

you said:  For my dataset, the length for the pair end is about 100bp ...

then in the log file of SOAPdenovo:  Insert size 300: 84425805 links input ...   This value is estimated in the program.

it is possible that you estimate the wrong insert size, which will reduce the map ratio.

Furthermore, both of the contig length and read quality will affect the performance of mapping.

2012/6/14 Jingjing Jin <jji...@mail.rockefeller.edu>

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[Yunjie Liu]

I think the contig set is too short for bowtie 

2012/6/14 刘兵行 <bingh...@gmail.com>

--
Sincerely,

Yunjie Liu

[Jingjing Jin]

You mean I should filter the short contig (<200bp) first, because most of the short contig may be the repeats.

For the configure file for my case is like this:

max_rd_len=90
[LIB]
avg_ins=300
reverse_seq=0
asm_flags=3
rd_len_cutoff=90
rank=1
pair_num_cutoff=3
map_len=32


q1=DNA1.fastq
q2=DNA2.fastq


If I estimate the insert size wrong, what is the reasonable value for the avg_ins parameter?

Thanks!

Jingjing
________________________________________
From: bgi-...@googlegroups.com [bgi-...@googlegroups.com] On Behalf Of Yunjie Liu [appl...@gmail.com]
Sent: Wednesday, June 13, 2012 10:20 PM
To: bgi-...@googlegroups.com
Subject: Re: [BGI-SOAP:467] SOAPdenovo

I think the contig set is too short for bowtie

2012/6/14 刘兵行 <bingh...@gmail.com<mailto:bingh...@gmail.com>>

you said: For my dataset, the length for the pair end is about 100bp ...
then in the log file of SOAPdenovo: Insert size 300: 84425805 links input ... This value is estimated in the program.

it is possible that you estimate the wrong insert size, which will reduce the map ratio.
Furthermore, both of the contig length and read quality will affect the performance of mapping.

2012/6/14 Jingjing Jin <jji...@mail.rockefeller.edu<mailto:jji...@mail.rockefeller.edu>>

The parameter I use for the bowtie is like this:

bowtie -S -p 2 --threads 16 --chunkmbs 1024 /SOAPdenovo_31_new/bowtie_index/oil_palm -1 DNA1.fastq_filtered -2 DNA2.fastq_filtered SOAP_contig_bowtie.sam

Do you think it is wrong?

Thanks!

JIngjing

________________________________________

From: bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com> [bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com>] On Behalf Of Ruibang Luo [luoru...@genomics.org.cn<mailto:luoru...@genomics.org.cn>]

Sent: Wednesday, June 13, 2012 9:57 PM

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Sincerely,
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[刘兵行]

From your configure file, you have set the possibly right insert size.

can you show us the contig length statistics lines including numbers, N50, average length and total length?

2012/6/14 Jingjing Jin <jji...@mail.rockefeller.edu>

[Jingjing Jin]

the log is like this:

96849486 edges in graph
there're 100636078 edges
after compacting 96871828 edges left
2198925 ctgs longer than 100, sum up 776671000bp, with average length 353
the longest is 27582bp, contig N50 is 786 bp,contig N90 is 124 bp
48446633 contigs longer than 32 output
time elapsed: 75m

In file: /diag/home/jjin/oil_palm/NGS/SOAPdenovo_31_new/pe.config, max seq len 90, max name len 256

8 thread created
96871828 edges in graph
read from file:
/diag/home/jjin/oil_palm/NGS/DNA/DNA/DNA1.fastq_filtered
read from file:
/diag/home/jjin/oil_palm/NGS/DNA/DNA/DNA2.fastq_filtered
current insert size 300, map_len 32
--- 100000000th reads
--- 200000000th reads
--- 300000000th reads
--- 400000000th reads
--- 500000000th reads
--- 600000000th reads
--- 700000000th reads
--- 800000000th reads
Output 431080384 out of 812531122 (53.1)% reads in gaps
748690134 out of 812531122 (92.1)% reads mapped to contigs
1 pe insert size, the largest boundary is 812531122

[LIB] 0, avg_ins 300, reverse 0
time spent on mapping reads: 8478s

overall time for alignment: 148m

scaff -g /diag/home/jjin/oil_palm/NGS/SOAPdenovo_31_new/oil_palm
there're 1 grads, 812531122 reads, max read len 90
K = 31
there're 96871828 edge in edge file
average contig coverage is 27, 20780502 contig masked
Mask contigs shorter than 33, 66150234 contig masked
139239197 arcs loaded
input 48446633 contigs
done loading updated edges
time spent on loading edges 601s

219914897 PEs with insert size 300 attached, 206386 + 3313590 + 0 ignored
estimated PE size 210, by 133357031 pairs
on contigs longer than 300, 110942082 pairs found,SD=73, insert_size estimated: 219
84425806 new connections
all PEs attached
time spent on loading pair end info 984s

75464691 link to masked contigs, 0 links on a single scaff
Insert size 300: 84425805 links input
Cutoff for number of pairs to make a reliable connection: 3
6454014 weak connects removed (there were 17922228 active cnnects))
392 circles removed
variance for insert size 30
a remove transitive lag, 84213 connections removed
a remove transitive lag, 0 connections removed
Picked 2864031 subgraphs,14080 have conflicting connections,2758081 have significant overlapping, 2659 eligible
maskRepeat: 1012341 contigs masked from 1225101 puzzles
a remove transitive lag, 18461 connections removed
a remove transitive lag, 0 connections removed
Picked 164027 subgraphs,2261 have conflicting connections,153297 have significant overlapping, 2 eligible
non-strict linearization
Picked 149646 subgraphs,4801 have conflicting connections,134374 have significant overlapping, 2 eligible
Masked 71233 contigs, 0 puzzle left
Freezing is done....
232 contigs recovered
all links loaded
time spent on creating scaffolds 644s

the final rank
563668 scaffolds from 2198900 contigs sum up 866316771bp, with average length 1536, 0 gaps filled
1260859 scaffolds&singleton sum up 984576421bp, with average length 780
the longest is 107724bp,scaffold N50 is 2404 bp, scaffold N90 is 324 bp


Should I change the avg_ins to other value and change the max_rd_len to the read length?

Thanks!

Jingjing
________________________________________
From: bgi-...@googlegroups.com [bgi-...@googlegroups.com] On Behalf Of 刘兵行 [bingh...@gmail.com]
Sent: Wednesday, June 13, 2012 10:28 PM
To: bgi-...@googlegroups.com
Subject: Re: [BGI-SOAP:469] SOAPdenovo

From your configure file, you have set the possibly right insert size.

can you show us the contig length statistics lines including numbers, N50, average length and total length?

2012/6/14 Jingjing Jin <jji...@mail.rockefeller.edu<mailto:jji...@mail.rockefeller.edu>>

You mean I should filter the short contig (<200bp) first, because most of the short contig may be the repeats.

For the configure file for my case is like this:

max_rd_len=90
[LIB]
avg_ins=300
reverse_seq=0
asm_flags=3
rd_len_cutoff=90
rank=1
pair_num_cutoff=3
map_len=32


q1=DNA1.fastq
q2=DNA2.fastq


If I estimate the insert size wrong, what is the reasonable value for the avg_ins parameter?

Thanks!

Jingjing
________________________________________

From: bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com> [bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com>] On Behalf Of Yunjie Liu [appl...@gmail.com<mailto:appl...@gmail.com>]

Sent: Wednesday, June 13, 2012 10:20 PM

To: bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com>

Subject: Re: [BGI-SOAP:467] SOAPdenovo

I think the contig set is too short for bowtie

2012/6/14 刘兵行 <bingh...@gmail.com<mailto:bingh...@gmail.com><mailto:bingh...@gmail.com<mailto:bingh...@gmail.com>>>

you said: For my dataset, the length for the pair end is about 100bp ...
then in the log file of SOAPdenovo: Insert size 300: 84425805 links input ... This value is estimated in the program.

it is possible that you estimate the wrong insert size, which will reduce the map ratio.
Furthermore, both of the contig length and read quality will affect the performance of mapping.

2012/6/14 Jingjing Jin <jji...@mail.rockefeller.edu<mailto:jji...@mail.rockefeller.edu><mailto:jji...@mail.rockefeller.edu<mailto:jji...@mail.rockefeller.edu>>>

The parameter I use for the bowtie is like this:

bowtie -S -p 2 --threads 16 --chunkmbs 1024 /SOAPdenovo_31_new/bowtie_index/oil_palm -1 DNA1.fastq_filtered -2 DNA2.fastq_filtered SOAP_contig_bowtie.sam

Do you think it is wrong?

Thanks!

JIngjing

________________________________________

From: bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com><mailto:bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com>> [bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com><mailto:bgi-...@googlegroups.com<mailto:bgi-...@googlegroups.com>>] On Behalf Of Ruibang Luo [luoru...@genomics.org.cn<mailto:luoru...@genomics.org.cn><mailto:luoru...@genomics.org.cn<mailto:luoru...@genomics.org.cn>>]

Sent: Wednesday, June 13, 2012 9:57 PM

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Sincerely,
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[Ruibang Luo]

Avoid provide free problem solving. Indicate what they could have been wrong.

rb

[Ruibang Luo]

Please notice that SOAPdenovo is a freeware that does not guarantee on anything so it's essential for users to get into it as much as possible for research purpose (avoid black box).
And we will release SOAPdenovo2 soon, we may put it on SourceForge, where the interactions between developer and users can be searched by other users with similar problems.

rb

[刘兵行]

estimated PE size 210, by 133357031 pairs
on contigs longer than 300, 110942082 pairs found,SD=73, insert_size estimated: 219 

the map ratio shown in log file is ok.

2012/6/14 Jingjing Jin <jji...@mail.rockefeller.edu>

[Axel Künstner]

> And we will release SOAPdenovo2 soon, we may put it on SourceForge, where the interactions between developer and users can be searched by other users with similar problems.

Do you have any timeframe for releasing SOAPdenovo2? I've tested SOAPdenovo and Allpaths-lg. It would be interesting to test SOAPdenovo2 on a medium sized vertebrate genome, too.

Greetings,
axel

[Ruibang Luo]

It's about to release in next month.
For you convenience, you can join out testing to use SOAPdenovo2 in advance to the formal publish.

rb

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[Albert J.Poustka]

Dear Ruibang Luo,

I d like to participate in testing soapdenovo2. Could you provide me a copy?

Greetings,

Albert

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[Axel Künstner]

Dear Ruibang,

I would be very interest to receive a copy of SOAPdenovo2 to test its performance.

Best regards,
axel

[Jingjing Jin]

Dear Ruibang,

I also would like to participate in testing soapdenovo2.

Could you provide me a copy?

Jingjing

On 2012/6/18 4:55, Albert J.Poustka wrote:
> Dear Ruibang Luo,
>
> I d like to participate in testing soapdenovo2. Could you provide me a copy?
>
> Greetings,
>
> Albert
>
>
> Am 18.06.2012 05:03, schrieb Ruibang Luo:
>> It's about to release in next month.
>> For you convenience, you can join out testing to use SOAPdenovo2 in advance to the formal publish.
>>
>> rb
>>
>>
>>
>> On 2012-6-14, at 下午9:12, Axel Künstner wrote:
>>
>>>> And we will release SOAPdenovo2 soon, we may put it on SourceForge, where the interactions between developer and users can be searched by other users with similar problems.
>>> Do you have any timeframe for releasing SOAPdenovo2? I've tested SOAPdenovo and Allpaths-lg. It would be interesting to test SOAPdenovo2 on a medium sized vertebrate genome, too.
>>>
>>> Greetings,
>>> axel
>>>
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>>>
>>>


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Lab of Plant Molecular Biology
Rockefeller University
1230 York Avenue
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[Richard Buggs]

I would also be interested in trying it,

best wishes

Richard

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[Ding Qiliang]

Dear Ruibang:

  

  I was wondering if I can participating in testing SOAPdenovo2.

  Best,

Andy  

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[Richard Buggs]

I have tried SOAPdenovo2 on some data I had previously assembled with the old version and seem to get significant improvement with the same options, (except the old verion was run with a minimum scaffold size of 100 and the new version with no lower limit):

old --> new

Number of scaffolds: 555042 --> 551925

No. of scaffolds over 100kb: 120 --> 290

N50 scaffold length: 14369 --> 18712

best wishes

Richard

On Monday, June 18, 2012 4:03:46 AM UTC+1, Ruibang Luo wrote:

It's about to release in next month.
For you convenience, you can join out testing to use SOAPdenovo2 in advance to the formal publish.

rb



On 2012-6-14, at 下午9:12, Axel Künstner wrote:

>
>> And we will release SOAPdenovo2 soon, we may put it on SourceForge, where the interactions between developer and users can be searched by other users with similar problems.
>
> Do you have any timeframe for releasing SOAPdenovo2? I've tested SOAPdenovo and Allpaths-lg. It would be interesting to test SOAPdenovo2 on a medium sized vertebrate genome, too.
>
> Greetings,
> axel
>
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[Yupeng]

Hi Richard,

Good news! Can you send me a copy of SOAP denovo2?

Thanks!

Yupeng

[Richard Buggs]

I think you need to ask Ruibang Luo

Richard

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[Yupeng]

Hi Ruibang,

Could you please send me a copy of SOAPdenovo2?

Thanks!

Yupeng

On Sunday, June 17, 2012 11:03:46 PM UTC-4, Ruibang Luo wrote:

It's about to release in next month.
For you convenience, you can join out testing to use SOAPdenovo2 in advance to the formal publish.

rb



On 2012-6-14, at 下午9:12, Axel Künstner wrote:

>
>> And we will release SOAPdenovo2 soon, we may put it on SourceForge, where the interactions between developer and users can be searched by other users with similar problems.
>
> Do you have any timeframe for releasing SOAPdenovo2? I've tested SOAPdenovo and Allpaths-lg. It would be interesting to test SOAPdenovo2 on a medium sized vertebrate genome, too.
>
> Greetings,
> axel
>
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[Alvaro Martinez Barrio]

Hi Ruibang,

Could I get a copy of that cunning SOAPdenovo2. It seemed to have
worked very well for Richard and I am about to run an assembly after
correcting my reads so I better go with SOAPdenovo2 from the beginning
instead.

Cheers!
álvaro

> For more options, visit this group at http://groups.google.com/group/bgi-soap?hl=en.
>



--

Alvaro Martinez Barrio
Department of Medical Biochemistry and Microbiology
Biomedicinska Centrum (BMC), Husargatan 3, C10:322b
Box 582, SE 751 23 Uppsala SWEDEN

Tel: +46 18 471 4502
Fax: +46 18 471 4673

[Bent Petersen]

Did you use the exact settings? Same kmer size etc?

Because I have been running some tests using plasmodium falciparum reads, and my N50 unfortunately dropped significantly...

Best,

Bent

[Li, Chenhong]

Hi, Ruibang,

Could you please send me a copy of SOAPdenovo2? I'd like to try it too.

Thanks!

Chenhong

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[Zhonghui Tang]

Hi Ruibang,

Could you mind send me a copy of SOAPdenovo2? I am interesting to play SOAPdenovo2 in advance.

Yours,

Zhonghui

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[Manoj Samanta]

Would love to get a testing copy, Ruibang. We discuss various NGS
related algorithms and programs in our blog -(http://www.homolog.us).
We can give a heads up to our readers on SOAPdenovo2, if you like.

[강양제]

Hi Ruibang,
Can I try soapdenovo2? Im working on plant genome and I might give you feed back about plant genome assembly.

Thanks,

2012. 6. 21. 오전 12:56에 "Yupeng" <liyup...@gmail.com>님이 작성:

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[Ruibang Luo]

Hi Bent,

Would you mind telling me which N50 is dropping?

從我的 iPhone 傳送

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[Ruibang Luo]

Hi Manoj,

Sure! The website is terrific.

從我的 iPhone 傳送

[Xiaofan]

Hi Ruibang,
Could you please send me a copy of SOAPdenovo2 also? I would like to try it on some fungal genomes. Thanks very much!
Best,
Xiaofan

On Monday, June 25, 2012 8:27:03 PM UTC-5, Ruibang Luo wrote:

Hi Manoj,

Sure! The website is terrific.

從我的 iPhone 傳送

Manoj Samanta <manoj....@gmail.com> 於 2012-6-19 18:46 寫道：

> Would love to get a testing copy, Ruibang.  We discuss various NGS
> related algorithms and programs in our blog -(http://www.homolog.us).
> We can give a heads up to our readers on SOAPdenovo2, if you like.
>
> --
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[Richard Buggs]

Hi Brent,

Yes, the same settings and kmer. I am assembling a 450Mb plant genome, so quite different.

Best wishes

Richard

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[Bent Petersen]

Hi Ruibang,

both my scaffold and contig N50 dropped...

Bent

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[kuhl]

Dear Ruibang,

we are involved in several vertebrate/plant genome projects and would be
very happy to have a test version of SOAPdenovo2.
Would you send us a version, please? Is there any support for long reads
(454/Iontorrent/Sanger) in the new version?

Best wishes,

Heiner


---------------------------------------------------------------
Dr. Heiner Kuhl
MPI Molecular Genetics Tel: + 49 + 30 / 8413 1551
Next Generation Sequencing
Ihnestrasse 73 email: ku...@molgen.mpg.de
D-14195 Berlin http://www.molgen.mpg.de
---------------------------------------------------------------

[Simo]

Dear Ruibang,

Could you please also send me a copy of the soapdenovo2? I'd love to test it using some of my current plant data. Thanks a lot!

Simo

On Sunday, June 17, 2012 11:03:46 PM UTC-4, Ruibang Luo wrote:

It's about to release in next month.
For you convenience, you can join out testing to use SOAPdenovo2 in advance to the formal publish.

rb



On 2012-6-14, at 下午9:12, Axel Künstner wrote:

>
>> And we will release SOAPdenovo2 soon, we may put it on SourceForge, where the interactions between developer and users can be searched by other users with similar problems.
>
> Do you have any timeframe for releasing SOAPdenovo2? I've tested SOAPdenovo and Allpaths-lg. It would be interesting to test SOAPdenovo2 on a medium sized vertebrate genome, too.
>
> Greetings,
> axel
>
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[Noa Sela]

Dear Ruibang,
Could you please also send me a copy of the soapdenovo2? I'd love to test it using some of my current Metagenomic data, Thanks!

Noa

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[Lo chienchi]

Hi Ruibang Luo,

I would like to participate in testing SOAPdenovo2. Could you please send me a copy?

Thanks,
Chien-Chi

[Oksana Riba]

Dear Ruibang,

We would like to test SOAPdenovo2 with several insect genomes.

Thank you.

Oksana

-- 

Oksana Riba Grognuz

Department of Ecology and Evolution (UNIL), Vital-IT (Swiss Institute of Bioinformatics)

UNIL Biophore office 4310, Phone: +41 (0) 21 692 4182