[VidJa]

Hi Boetie,

Do you plan to include the use of SAM/BAM as output instead of the default bowtie, that way you clould dropin all sam/bam capable aligners, like BWA (for longer reads with the sw option), Smalt http://www.sanger.ac.uk/resources/software/smalt/
or Stampy http://www.well.ox.ac.uk/project-stampy
and probably a full bag of other aligners.

[SLB]

Hi Boetsie,

Thanks a million.

Cheers,

Stephen

Hi SLB,

At the moment not, but in the next version i'm planning to include this option as well as multithreading bowtie.

For the moment, you can change the code and do it yourself . Go to the 'bin' directory and open the file MapWithBowtie.pl. Now go the lines starting with 'system'

Change the -v 0 to your required number of gaps, for example -v 2 allows two gaps.

For gapped mapping of the reads on the contigs for extension, change the first line starting with system("$bowtiepath ...
For gapped mapping of the reads on the contigs for scaffolding, change the second line starting with system("$bowtiepath ...

Boetsie

[boetsie]

Is it possible to change the bowtie options to allow mismatches?

Hi SLB,

At the moment not, but in the next version i'm planning to include this option as well as multithreading bowtie.

For the moment, you can change the code and do it yourself . Go to the 'bin' directory and open the file MapWithBowtie.pl. Now go the lines starting with 'system'

Change the -v 0 to your required number of gaps, for example -v 2 allows two gaps.

For gapped mapping of the reads on the contigs for extension, change the first line starting with system("$bowtiepath ...
For gapped mapping of the reads on the contigs for scaffolding, change the second line starting with system("$bowtiepath ...

Boetsie

[SLB]

Is it possible to change the bowtie options to allow mismatches?

[boetsie]

hi boetsie,

First, SSPACE is a great piece of software. Hands down, it's the easiest to use and most efficient scaffolder I've found and gives great results. Thanks for all your work.

I have a question about the -t parameter. After clipping up to -t bases, does SSPACE try to extended contigs again?

thanks,
ajtritt

Hi ajtritt,

thank you so much for this nice comment! Good that it gives great results for you, and I'm glad it could help.

To clearify about the trimming (-t option); SSPACE does not first clip up to -t bases. It first tries to extend. Then, if it can no longer extend a contig, it will try to trim bases and try to extend them again. This will go through until no more extension can be done as well as the trimming does not lead to further extension.

Kind regards,
Boetsie

[ajtritt]

-t parameter

hi boetsie,

First, SSPACE is a great piece of software. Hands down, it's the easiest to use and most efficient scaffolder I've found and gives great results. Thanks for all your work.

I have a question about the -t parameter. After clipping up to -t bases, does SSPACE try to extended contigs again?

thanks,
ajtritt

[SLB]

I am just interested if anyone has been playing around with the parameters of SSPACE (k, a,) and has any insights.

Cheers,

Stephen

[boetsie]

Hi, I am just trying out SSPACE at the moment for a large genome (2.7Gb) using contigs assembled from abyss and a number of 3,5 and 10Kb mate pairs. Is there any way of getting SSPACE to accept compressed files as input?

hi SLB,

i'm sorry but this is currently not possible.

Boetsie

[SLB]

input files

Hi, I am just trying out SSPACE at the moment for a large genome (2.7Gb) using contigs assembled from abyss and a number of 3,5 and 10Kb mate pairs. Is there any way of getting SSPACE to accept compressed files as input?

[boetsie]

SSPACE is very nice tool for us. Thank you for your good job.

By the way, what should I call SSPACE?

es es pace?
es pace?
es space?

Regards.

I'm sorry, i had not seen this question before, i must have missed it. You can call it 'es space'

Boetsie

[boetsie]

Hi davfre,

i'm sorry, i've not included this functionality yet. Also, It is not possible to include TAB-delimited files in SSPACE. Reason is that I did not have much time to work on this. I hope to do so in the near future, it is on my to-do list

Kind regards,
Boetsie

[davfre]

I, too, would like to include BAC end sequences (Sanger seq) to scaffold pre-assembled contigs/scaffolds. I had trouble running Bambus (due to the requirement for a .contig file) and found SSPACE. However, Bowtie fails to map a majority of long reads due to indels/accumulation of mismatches in the long reads, so I would rather like to use (the best) mappings from bwa-swa, blat or another tool.

Did anyone already solve the issue of either reading sam files, or convert those to the simple tab delimited format asked for by SSPACE? Would be great, as most aligners can output sam or be converted to that format with existing tools.

[boetsie]

Hi jstjohn,

in the 'reads' folder there are 2 files generated per library.

*.filtered.readpairs.singles.fasta extension is the filtered file during reading of the paired-read files. This file is filtered on paired-sequences containing N's. If one of the two sequences of a pair contains an 'N' character, the paired-read is discarded.

*.foundpairedreads extension contains the paired-reads used for scaffolding. Keep in mind that we only use the edges of the contigs for mapping the reads, therefore less reads can be mapped (though we don't mind, because they are not very useful for scaffolding).

Sorry that this was not clear.

Boetsie

[jstjohn]

file in ./reads/ folder really small

Hey,
I am a little worried because my input files were each about 3G of gzipped fastq, and the .fasta files in the ./reads/ folder are only about 100M each. I am pretty sure that there are more perfect reads without N's than that... I trimmed bases from the beginning and end of reads prior to running the program, and the file should only have reads that are over 30nt.

One possible bug is that I noticed a few of the fastq reads have 0 length in my input file, but they are still paired properly, and have the right new lines and everything so the two files are the right relative length. Do you think that is causing issues for the program?

UPDATE: fixed the above issue with the few 0 length reads, and the output files still have this issue of being very small compared with the size of the input files. Maybe I just don't understand what the files in the ./reads folder are?

Thanks!
-John

[boetsie]

Hi themwg,

thank you for the good points you mention there. I see indeed some vague descriptions and mistakes in the summary file.

About your questions;

- I indeed take 4500bp from the left and right edge for scaffolding, which is of course the obvious method.

- You are absolutely right, the number of pairs should indeed be at least two times smaller than the number of single reads. I see that I displayed the wrong variable in my script. I will fix this in a next release.

- As said above, wrong calculation for the total number of single reads. Total pairs is a sort of filtering step for the pairs. The actual pairs used for scaffolding is the value given at "Assembled pairs".

I'm sorry for the mistakes, as said, i will fix this in next release which will probably come in the next week.

Kind regards,
Boetsie