I am very new to genome assembly and teaching myself about pre-assembly QC steps.
I performed fastQC analyses on HiSeq4000 data for forward...
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Understanding FastQC output before Vs after trim_galore
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mutationalMeltdown started a topic Assigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?in MetagenomicsAssigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?
I'm interested in identifying bacterial pathogens from shotgun metagenomic data. Crudely, I envisage the pipeline to be something like this:
1)... -
k-mers in the middle of the read
Hi All,
I'm new to RNASeq analysis and am looking for some advice on the FastQC k-mer output.
For several of my samples,... -
calculus of kmer coverage per chromosomes
Hello everybody
I am trying to find a method to calculate the kmer coverage for each chromosome. I tried genomeCoverageBed and it seems... -
Illumina HiSeq k-mers
Hi
This is about the Illumina Hiseq based on Trueseq library.
Prior to trimming, the fastqc showed some k-mers enrichment in the... -
SPAdes: selecting K-mer based on read length
Hello Members,
I need your guidance in selecting k-mer for assembling bacterial genome, paired end using SPAdes.
I know and have read...Last edited by bio_informatics; 04-14-2015, 05:08 AM. -
Clustering of samples based on tetra nucleotide frequency
Hi All,
I have assembled several metagenomic samples of various sequencing depth. The contigs have been annotated with COG. Now I want... -
NGS data-QC, Kmer, Genome size finding
I am new to NGS, I have just received sequenced raw files of non-model plant from Hiseq. I would like to know sequence quality check for quality filtering.... -
meta-velvet returns nodes instead of contigs in assembly?
Hi I just started using meta-velvet to assemble a small metagenome 100k. The average length of reads are 102, with a min of 29 and a max of 227. I tried... -
How to remove the reads whose k-mers are more or less than an abundance threshold
Hi everyone,
I am a newbie to this forum. I have been dealing with the 100Gb data from the Illumina Hiseq 2000 recently. Before assembly, I want... -
K-mers
Hey all,
I am an undergrad who is just getting into bioinformatics and I am looking to understand a little bit more about NGS and assembly...
