Hello all,
After trimming raw reads, I have tried to assemblied my NGS data by several assemblers.
As you can see in the picture, I got the different result from the different assembler. In my opinions, the assembly draft by Velvet was not so good.
The drafts by SPAdes demostrated the excellent results (N50, L50, longest contig, etc.), but the numbers of mismatches and misassemblies were not good as those of ABySS (the first and second columns).
My questions are...
- Which one is better in your opinion?
- Is it possible to correct the mismatches and misassemblies?
- How can I do to improve my assembly draft?
Thank you.
•
written
by
Tong •
1 answer
Evaluating an assembly is not so straightforward.
There are a few commonly use measures, largest contig, N50 and so on.
Read up on the methodology employed by the assembly contest called Assemblathon to get a sense of the various tradeoffs that need to be accounted for
Log in to answer this question.
-
How to validate the assembly completeness of unaligned reads ?
written by Sony Nguyen •
-
How to generate Metaassembly for a genome?
written by sunnykevin97
-
Assessment of the genome assembly
written by siu
-
What is the normal N50 range when assembly the virus genome.
written by FAST_GENOME
-
Spades vs Velvelt_why do I get much more contigs with SPADEs?
written by anna •
-
Short-long read hybrid de novo assembly - determine k-mer size
written by Kenny •
-
de-novo whole genome assembly and annotation
written by kratiranjan2020 •
-
Tutorial: InsideDNA: Benchmarking seven most popular genome assemblers
written by shilparaopradeep •
-
Choosing Optimal Assembly from Quasta Data
written by RichelleRedekop •
-
Genome Assembly From Large Insert Libraries
written by Rahul Sharma
