I have many reads from chicken growth hormone and I want to assemble these reads to form contig and to complete the whole sequence of chicken growth hormone in Iraqi native chickens.
If you plan to assemble the reads into contigs, I suppose already you have clean/trim your reads using the viewer FastQC and Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) as example. Otherwise you may have to start first to check reads quality before proceeding with the assembly.
I suppose you are looking for chromosome rearrangement or something similar, then novo-assembly makes sense. Here is a bench of tools, select the once matching your reads sequence technology and length.
https://omictools.com/genome-assembly-category
Let me know if you need any assistance.
Cheers.
First, you need to check the quality of your reads (FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trim them if required (https://wiki.hpcc.msu.edu/display/Bioinfo/Trimmomatic). If your reads are obtained fron RNA-Seq, so you can assemble the reads by doing de novo-assemly using Trinity approach (follow the instructions: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875132/).
Please let me know if you need further info.
I currently used a very convenient software called "CodonCode Aligner" (http://www.codoncode.com) for alignment. It allows you to do all those mentioned steps (quality control, end clipping, trims etc.). You can easily find mutations, Indels etc, assamble contigs, align to reference sequences and so on. While it is quite expensive - if you plan to use it often it may well be worth the prize. If you just need it to finish this one project - they have a 30 days trial period. Hope that helps.
Good luck,
Klaus
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