Hello,
I have paired end and mate pair reads from illumina. My expected genome size is about 1 GB. I'm not a bioinformatician and I'm trying to figure out how to assemble my data.
1) Do you have any recommendation for a software ?
2) For paired end data, is it worth to merge it with a tier software or is it done with the assembler ?
4 answers
There was a big project Assemblathon that published a thorough review of different assemblers: http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-2-10
They used three different species with 1.0-1.6 Gb genomes, so it's especially relevant in your case.
I have used the BBmap toolset to get some initial information in paired-end data and then use those parameters to run the data through trinity to produce the final assembly. I would also recommend running it through TransDecoder to find ORFs.
You can use Abyss assembly program using both mate pair and paired end reads. Recent wheat genome survey sequences were assembled using it. You can also use SOAPdenovo. Have seen assemblies of 4Gb assembled with it. You need to try different k-mer assemblies to get the sweet spot for your data.
2) For paired end data, is it worth to merge it with a tier software or is it done with the assembler ?
You mean merging the forward and reverse reads by overlap. The two programs I mentioned takes two separate files for forward and reverse reads. You dont need to merge them.
Log in to answer this question.
-
Difference between mate-pair, paired-end and long read
written by Chvatil
-
Hybrid assembly PacBio Illumina in 2018 ?
written by Picasa
-
Scaffolding assembly contig with various Mate pair Library Inquiry
written by edge •
-
Assembling de novo with multiple versions of paired-end reads
written by kingcohn •
-
Hybrid assembly of PacBio and Illumina reads
written by int11ap1
-
Best de novo assembler for insect genome ?
written by Picasa
-
Assenbly and mate pair processing ?
written by Picasa
-
How much computing resources does an ABySS run take
written by muralis.bio •
-
Mate Pairs Contaminated With Single And Paired End?
written by Adrian Pelin
-
Denovo Assembly Of Paired And Mate Paired Reads
written by sebabiokr •
I used Spades and I've had good results with it.
SPAdes is great, but is designed for bacterial assemblies, which is probably not the case here based on the genome size.
I am trying to use SPAdes with a bacterial genome, also having Paired-end and Mate-pair, cannot find out how to adapt the Mate-pair reads since SPAdes only accepts "high quality reads" (also having this problem with IotTorrent mate-pairs. How are you doing this? Thanks