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Thread | Thread Starter | Forum | Replies | Last Post |
Threshold quality score to determine the quality read of ILLUMINA reads problem | edge | Illumina/Solexa | 35 | 11-02-2015 11:31 AM |
SPAdes: erroneous kmer threshold | bio_informatics | Bioinformatics | 9 | 05-17-2015 06:03 PM |
how to set SNP QUAL threshold | volavii | Bioinformatics | 0 | 07-08-2013 07:47 AM |
how to determine the RPM threshold for MeDIP | zchou | Bioinformatics | 0 | 12-01-2011 02:52 AM |
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#1 |
Member
Location: South Korea Join Date: Apr 2014
Posts: 10
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Hi,
Thank you for developing SPAdes for hybrid assembly. I tried to assemble Illumina pair-end with Oxford Nanopore Sequence for plant mitochondrial genome assembly. Before carried out, I used BBMAP to trim adapters and normalize Illumina data. I have used the commands for trim adapters: bbmap$ ./bbduk.sh -Xmx1g in=read1.fastq in2=read2.fastq out=trim_read1.fastq out2=trim_read2.fastq ktrim=r k=23 mink=11 hdist=1 ref=resources/adapters.fa tbo tpe for normalize: $./bbnorm.sh in=trim_read1.fastq in2=trim_read2.fastq out=norm_read1.fastq out2=norm_rread2.fastq target=100 min=5 Then, I used these Illumina pair-end reads with Oxford nanopore and the commands as follows: $ ./spades.py -k 99 --pe1-1 norm_read1.fastq --pe1-2 norm_read2.fastq --nanopore nano_read.fastq --careful --cov-cutoff 90 -o hybrid_assembly -m 188. When I run using this command, I have got an error message as: ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 8:48:41.078 34G / 56G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable * 8:48:41.472 34G / 56G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 22 * 8:48:41.477 34G / 56G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 22 I am herewith enclosing spades.log file for your reference. Please find and suggest me what could be the problem and how to solve it.. Thank you. |
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Tags |
bbmap, hybrid assembly, illumina & 454, nanopore miniion, spades |
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