So one way I can see it is that first i should make a Qual file with a numerical value of 50 for each nucleotide and then merge sequence and quality files to FASTQ using this code http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ
Assembling Sequences Without The Fastq File
I have been given a fasta file having short map reads obtained from some next generation sequencing method i have not been provided with the fastq file.What would be the best tool or best way to assemble these sequences either denovo or using a reference database. I was looking at bioperl howto : Short-read assemblies with BWA but it seems that it requires fastq files too. Please let me know the best way to go about in getting the best assembly possible.
• 5,286 views
•
link
updated
by
Michael Schubert
•
written
by
Saad Khan
•
written
by
Saad Khan
2 answers
An idea: if you don't have the qualities of your reads(!), you could create a dummy fastq file with an average quality for all the bases and then use the standard software for assembling the genome ?
• 2 views
•
link
updated
by
Ram
•
written
by
Pierre Lindenbaum
•
written
by
Pierre Lindenbaum
Another idea: contact your supplier and ask for the fastq file.
If that's not an option, MIRA can do assemblies on fasta files. Velvet too, if I recall correctly.
• 1 views
•
link
written
by
Michael Schubert
Btw, I'm aware that BWA aligns to reference genomes and those are primarily de novo. But you haven't told us if you plan to align reads to reference, contigs to reference, or have a reference at all ;-)
• 0 views
•
link
written
by
Michael Schubert
I do plan to use a reference genome. What if I do what Pierre suggested by making a Qual file with a numerical value of 50 for each nucleotide and then merge sequence and quality files to FASTQ using bioperl code (possibly decreasing quality at the end).Which one would be better using MIRA or using hypothetical quality
Actually I am doing the assembly of a baculovirus, there are many genomes available at NCBI belonging to family baculoviridae. Are there specific assemblers for prokaryotic or small organisms, currently I am trying my hand with minimus which is a part of AMOS package. Please let me know what all I can do with the assembled genome.
• 0 views
•
link
updated
by
Ram
•
written
by
Michael Schubert
•
written
by
Michael Schubert
Velvet has an excellent documentation on the website. Just look it up.
• 0 views
•
link
written
by
Michael Schubert
Log in to answer this question.
More posts like this
-
Coverage calculation prior to a genome assembly-BBTools
written by GLR •
-
Assemblying Sanger traces and error threshold
written by nchuang
-
Variant calling and linkage disequilibrium when using de novo assembles
written by avismirabilis •
-
Strategy to get rid of fake mate pairs
written by Adrian Pelin
-
Choosing Optimal Assembly from Quasta Data
written by RichelleRedekop •
-
Bwa or bowtie for mapping mulitple genomes
written by williamjohn360
-
Assessing Quality And Accuracy Of De Novo Genome Assembly
written by a81526a •
-
Genome Assembly From Large Insert Libraries
written by Rahul Sharma
-
Programs/Parameters For De Novo Transcriptome Assembly Of Ion Torrent Reads?
written by Ahdf-Lell-Kocks •
-
Cnv Calling Methods For The Illumina Omni2.5 - Penncnv And Quantisnp Possible?
written by Ryan D
BWA maps reads to a reference, and you should be able to do that by just adding fake qualities, like Pierre suggests - possibly using decreasing quality towards the end of the reads. Many de novo assemblers ignore quality anyway (typically using de bruijn graph assembly), but I haven't been able to get very good results from them.