I am working on a project at my university which uses multiple genome assemblers, including SOAPdenovo.
I have noticed however I am unable...
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SOAP Genomics Deprecated?
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Introducing BBNorm, a read normalization and error-correction tool
I'd like to introduce BBNorm, a member of the BBTools package.
BBNorm is a kmer-based normalization tool for NGS reads, which may also be...Last edited by Brian Bushnell; 01-29-2015, 09:47 AM. -
on SOAP program
Hi everyone,
I just typed 'make' to install SOAP, but I got this error.
main.c
.text.startup+0xff): undefined reference...
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Setting up Linux for SOAP de novo
Hey all,
I'm new to WGS and need some help getting my computer set up.
From a clean install of Ubuntu 14.04 x64, what packages... -
SOAP Fusion with mm10
I'd like to use SOAP fusion with mm10, but I haven't been able to create the NMtoTreeFam file required. This file is a conversion table between UCSC IDs,... -
SOAPdenovo command not found error (linux)
Hi Everyone !
I'm new to this field of genome sequencing and generating contigs.
I've downloaded the latest bin version of SOAPdenovo2 and... -
SOAPsnpZ error : 'std::out_of_range'
Gday all,
I am attempting to use SOAPsnpZ to call SNPs from SOLiD data that I aligned using SOAP2. After conducting the alignment I 'sorted'...Last edited by ashNZ; 10-09-2013, 06:21 AM. -
SOAP denov "missing reads"
Hi there,
my question is about denovo assembly using SOAP denovo-trans. I have data from a MiSeq, 20 Mio paired end reads, 250bp each,... -
Bowie outputs very few alignments
Hi,
I am trying to map my contigs, in fasta format, assembled using velvet from a 454 single read data. After the assembly i tried to reconfirm... -
soap2 warning: length y <0 skip anyway
Hi all,
I have encountered a problem with soap2, when I would like to map my 17-30nt reads to genome (both fasta).
I used default parameters... -
SOAPsnp install problems
I tried to use SOAPsnp to call SNPs for RNA-seq data. When I used "make all" to install the SOAPsnp, it come out such words:
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SOAPdenovo map question
Dear fellow sequencers,
I am trying to assemble some reads using SOAPdenovo and map the reads to the assembled contigs. In SOAPdenovo,... -
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... -
kmer vs accuracy
Hi,
Given below is an explanation that i found for the different kmer size and its effect on sensitivity and specificity.
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SOAP:segmentation fault
Hi All,
I am trying to map solexa PE reads (fastq) from different strains onto reference scaffolds file (fasta) using soap2. The questions I have...
