Re: Redundans

[l.p.p...@gmail.com]

Hey Intikhab, 

Thanks for interest in Redundans. I have a few recommendations: 

I have a diploid plant genome with expected size of 2GB. I have 50 cells pacbio sequenced and one run of illumina 25000.

I had an initial go with spades with and without pacbio reads. Number of contigs resulted were quite high.

Definitely try Platanus for de novo assembly of large, plant genomes. I'd recommend running platanus with just a few Illumina paired-end libraries first, then do scaffolding with the rest (including long reads). Throwign everything to the assembler usually results in poorer assemblies than doing just what I've said. 

And then run redundans with all libs. 

 

Tried using illumina contigs, illumina reads, a closer reference and pacbio reads via redundans. First it was failing on fastq2sspace , no space left on device. We fixed it by writing not into temp but into current directory. Now it says:

Can you send me an exact command you are using? 

 

Welcome to SNAP version 1.0beta.23.

Loading index from directory... Unable to open file 'IBL_redundans_ref_long_short_reads_scaffolds_noreductions__2/contigs.fa.snap/GenomeIndex' for read.

Index load failed, aborting.

Aligning.

seems index was not loaded from directory by SNAP, how big is this problem? How much memory should I allow and number of cpus? I am allowing at present 250GB ram and 64 CPUS.

That's odd, SNAP requires up to 10x more memory than the genome size in GB ie. ~30GB for human (3Gb), so for you 20-40 Gb should be sufficient. 

 

Any help will be appreciated.

General log says:

##################################################

[Wed Sep 27 22:50:10 2017] Estimating parameters of libraries...

 Aligning 279357551 mates per library...

Insert size statistics                          Mates orientation stats

FastQ files     read length     median  mean    stdev   FF      FR      RF      RR

/scratch/dragon/intel/cbrc-PrlMill_Babil/Data/Interm/Assemblies/IlluminHiseq2500/29A/S_17_690_Pm-IBL_AD12_L008.A5SpadesAssembly/S_17_690_Pm-IBL_AD12_L008.assembly.s2/S_17_690_Pm-IBL_AD12_L008.assembly/corrected/S_17_690_Pm-IBL_AD12_L008.assembly.ec_1.00.0_0.cor.fastq.gz /scratch/dragon/intel/cbrc-PrlMill_Babil/Data/Interm/Assemblies/IlluminHiseq2500/29A/S_17_690_Pm-IBL_AD12_L008.A5SpadesAssembly/S_17_690_Pm-IBL_AD12_L008.assembly.s2/S_17_690_Pm-IBL_AD12_L008.assembly/corrected/S_17_690_Pm-IBL_AD12_L008.assembly.ec_2.00.0_0.cor.fastq.gz   125     417     427.17  85.44

   4       9720    273     3

##################################################

[Wed Sep 27 22:51:41 2017] Scaffolding...

 iteration 1.1: IBL_redundans_ref_long_short_reads_scaffolds_noreductions__2/contigs.fa 2426611 1396787756      48.607  182615  795059649       1911    193     0       97707​

Can you list a output directory for me (ls -lah redundans_out)?  

btw: you can write directly to Redundans google group <redu...@googlegroups.com>.

Thanks for feedback!

L.  

Many Thanks for help and clues.

Best,

IA

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Intikhab Alam, PhD

Research Scientist
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Thuwal 23955-6900, KSA
W: http://www.kaust.edu.sa
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[Fuyou Fu]

Hi Pryszcz,

I have used Redundans. The assembling result can improve our genome assebling. I read your email. I have confused one suggestion for Intikhab a little bit.

 I'd recommend running platanus with just a few Illumina paired-end libraries first, then do scaffolding with the rest (including long reads).

what is it your mean about do scaffolding with the rest? My understand is what you said that do scaffolding with rest (including long reads) use Redundans, not other software. Because I did it like this.

Thanks,

Fuyou

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Fuyou Fu, Ph.D.
Department of Botany and Plant Pathology
Purdue University
USA

[l.p.p...@gmail.com]

in platanus you can run assembly and scaffolding / gap closing with different libraries (separate programmes). alternatively just get contigs and run Redundans. both approaches are valid :) if you have time & resources, I'd try first :)

L. 

L.

[Fuyou Fu]

Thanks,

I got it.

Fuyou