genome assembly for a pathogens
Hello, I have an assembly with a big size (3.8MBP) than expected (2.3-2.8). There is a high number of contigs (1119) than accepted (500). seems to be contamination. Is there way to remove other contaminating contigs or should we discard the assembly. any recommendations.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Removing contamination of set of genes from selected cell clusters
written by singcell •
-
de novo assembly: should I discard contigs below insert size?
written by smo •
-
Detecting Chimeric Contigs
written by KSS •
-
Assembly quality check
written by tothepoint
-
Criteria for filtering contigs after spades assembly
written by fhsantanna
-
Rescaffolding a genome assembly?
written by cmdcolin
-
Transcriptome Assembly with rnaSPAdes
written by biofalconch
-
Average coverage of de novo SPAdes assembly deviates a lot from theretical coverage
written by ALchEmiXt
-
Subsetting fasta files based on blast results
written by dpearton •
-
Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
written by Rayan Chikhi
A quick way you can check for contamination is by aligning the assembly to other genomes (as it seems you have some available) and/or BLAST the contigs against NCBI, particularly those that do not align in the first step.
You can also use a metagenomic tool like Kraken2 with one of their many databases to try and identify contamination on your adapter trimmed reads. Also, a high number of contigs could just mean you don't have reads long enough to span repetitive or complex genomic elements.
What was your sequencing strategy?