19 results in 0.0021 seconds.
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issue changing predetermined K values on SOAPdenovo2
I am currently using SOAPDENOVO2 on a supercomputer with SLURM queuing system to perform a de novo assembly from FASTQ paired-end files with genomic DNA... -
GapCloser using SOAPdenovo
Hey everyone!
I'm a rookie in these bioinformatics things.
I've been running my first genome assembly during these last couple... -
What is the effect of modulating the gaplenDiff parameter -G in SOAPdenovo2?
Hello Seqanswers! Long time reader, first time questioner.
I'm trying to figure out what the effect of changing the gaplenDiff parameter... -
Finding repetitive elements from BAC sequences and Illumina sequences.
Hello to everybody,
I need to identify repetitive elements of 5 genotypes from the same species (a plant species that is not yet sequenced).... -
SOAPdenovo configuraion file
Hello,
I just got the raw reads from Illumina Hi-Seq (2 files: 1 forward and 1 reverse). I want to do the assembly with SOAPdenovo. I cannot find... -
SOAPdenovo running for 48 h?
Hi,
I am doing do novo assembly of a bacterial genome ~4Mb. I used Abyss and it took around 8 hours to produce ~1000 scaffolds (N50 80kb).... -
some trouble with SOAPdenovo, my assembly and the BGI output
Hi there,
this is my first post in SEQanswers but I looked the community from long time.
I started these last 6 month to work with metagenomics... -
SOAPdenovo and FASTA files - Newbie question
I'm a newbie when it comes to NGS bioinformatics. I'm testing SOAPdenovo with a small FASTA file (3300 kb). The FASTA file is an unpaired set of exported... -
SOAPdenovo and FASTA files - Newbie question
I'm a newbie when it comes to NGS bioinformatics. I'm testing SOAPdenovo with a small FASTA file (3300 kb). The FASTA file is an unpaired set of exported... -
Soapdenovo stops at reading reads
Hi everyone,
I have 1 billion reads from Illumina GA and have been trying to run an assembly for a 0.8 Gb genome using Soapdenovo v 1.05.... -
SOAPdenovotrans file read error
I am trying to assemble paired read illumina data using the config file:
[LIB]
max_rd_len=100
asm_flags=3
rank=1... -
KmerFreq - std::bad_alloc
I am new to SOAPdenovo and am still learning, so please help out this newbie.
I am running a PBS script to run KmerFreq before running SOAP. I... -
pair_num_contigs in SOAPdenovo assembly
All,
I'm running SOAPdenovo 1.05 and it seems to be ignoring when i set the pair_num_contigs parameter in the cfg file. I try setting this to... -
Problem Encountered When Using SOAPdenovo: Floating Point / Segmentation Error
Hi, Dear Colleagues:
I'm a student from Fudan University, and is currently trying to use SOAPdenovo to run de novo assemble on human mitochondrial...Last edited by andyding; 11-22-2011, 04:33 AM. -
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...
