9 results in 0.0023 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... -
SOAPdenovo2 long run
Hello all,
I’m trying to assemble a plant genome (this is my first time). I have 100bp PE reads (106G forward and 106G reverse).... -
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... -
Unexpected SOAPdenovo2 behavior - contigs conflict with scaffolds
We are presently working on the sequencing and assembly of a draft genome of a ~1 Gb invertebrate. The preliminary dataset is a HiSeq single lane of PE100,... -
How to use unpaired reads from trimmomatic output in SOAPdenovo for assembly?
Hi all,
I have illumina paired end reads trimmed using Trimmomatic - resulting in 4 files - 2 paired, 2 unpaired (as expected). Now I want... -
SOAPdenovo2 Ambiguous output redirect.
Currently using SOAPdenovo2 and used submission form below:
...Code:#!/bin/bash #$ -cwd #$ -N SOAPdenovo2 #$ -e /ibers/ernie/groups/rumenISPG/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/SOAPdenovo2.error
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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... -
How excatly does SOAPdenovo2 calculates the total scaffold length?
Hi there!
I've been working with SOAPdenovo2 quiet a while now.
For some extra researches, I took a closer look on the outputfile... -
SOAPdenovo2 standard deviation input?
Hi there!
Within SOAPdenovo2, where can i insert the standard deviation of my average insert size?
Thank you and Best regards,...
