I am trying to make something out of a denovo, heterozygous plant WGS.
it won't go past a contig stage (scaffolding improved average contig length...
15 results in 0.0029 seconds.
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localized consensus build instead of scaffolding
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Scaffolding tools for metagenomics ???
Hello,
I´m currently working on paired end data (2*150) to build a metagenomics assembly.
So far i´m using the combination of...Last edited by danova; 02-09-2016, 05:00 AM. -
Remove subset of good reads to improve genome assembly
Hello seqanswers,
I'm de novo assembling a diploid genome (haploid genome = 200Mb) with reads from Illumina Hiseq V4 2x125 (high-output)... -
Tool to find reads bridging two scaffolds?
I have a set of PacBio reads and I need to find which of them actually bridge two scaffolds of an existing assembly.
So far I've tried blasting... -
method for superscaffolding
We have a eukaryotic diploid genome assembled and scaffolded using ALLPATHS-LG. In addition, we have a linkage map generated from iso-crossing individuals... -
Combining de novo assembly and reference scaffold
What is the best way to combine de novo and reference-guided assemblies? The scaffold of a closely-related species is available and I would like to use... -
Finding a gene of interest in a scaffold
Dear all,
I'm having my first go with working with a newly sequenced genome. I have a bacterial genome sequence in scaffolds assembled... -
bambus scaffolds on two mate pair libraries
Hi mira/bambus users,
we are running mira on hybrid libraries from 454 and illumina sequencers. To get nice scaffolds we are using bambus,...Last edited by dragon0711; 01-15-2013, 07:50 AM. -
gsMapper failed to create ace or bam file
Hi,
I encountered a problem with gsMapper (v2.6) when I tried to align 10M Illumina paired end reads on to 100 large contigs. Even though... -
SOAPdenovo for ABySS contigs
Dear All
I am using ABySS to generate contigs from human reads. I now want to make scaffolds from it. I used SSPACE but did not get as... -
Mira assembler: Medium sized genomes;How to use 2 separate files for paired-end reads
Hi all,
This is Nandan Deshpande from UNSW, Sydney, Australia.
I am working trying to assemble a eukaryotic genome of estimated... -
IMAGE2 input and parameters
I am able to run IMAGE2 after creating read.placed.original and contigs.fa.original in the required format. Here are my questions:
* Is it... -
Scaffolding problem
Hi,
I have these scaffolds with different sizes(1 to 200 kb) from a previous assembly.
Now there is some new data with... -
Scaffolding tool
Do you know any scaffolding tool targeted to NGS plattaforms? I am looking for something that can use contig fastas and aligned paired ends (eg SAM format)... -
Scaffolding output from a velvet assembly of SOLiD data
Hi,
I'm working on de novo assembly of a complex genome. I've been using velvet to generate the assembly of paired reads from SOLiD and...
