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Dear SeqAnswers users,
I'm a systematist VERY new to NGS, both in terms of lab and analytical methods. I'm wondering if anyone has some suggestions on how I should proceed. My goals are to generate complete plastomes for annotation and phylogenomic analysis.
I have been working with de novo and reference guided assemblies (already generated by someone else) and trying to get these to contig. I have been using Sequencher to do this for one of my reference guided assemblies (a series of 20 contigs), with very limited success, and Dogma to visualize which pieces of the chloroplast genome are represented by the contigs. I can't seem to get Sequencher to "close the loop," i.e. give a complete plastome assembly; I assume there are gaps between my contigs that need to be filled.
I wonder if there is software that will allow me to visualize ALL of my contigs at once, perhaps aligned to a reference sequence. I want to be able to see the "gaps" between my contigs so I can amplify and Sanger-sequence these regions to close the circular genome.
Also, how do people usually deal with the inverted repeat in the chloroplast genome?
Any suggestions will be very much appreciated!
I'm a systematist VERY new to NGS, both in terms of lab and analytical methods. I'm wondering if anyone has some suggestions on how I should proceed. My goals are to generate complete plastomes for annotation and phylogenomic analysis.
I have been working with de novo and reference guided assemblies (already generated by someone else) and trying to get these to contig. I have been using Sequencher to do this for one of my reference guided assemblies (a series of 20 contigs), with very limited success, and Dogma to visualize which pieces of the chloroplast genome are represented by the contigs. I can't seem to get Sequencher to "close the loop," i.e. give a complete plastome assembly; I assume there are gaps between my contigs that need to be filled.
I wonder if there is software that will allow me to visualize ALL of my contigs at once, perhaps aligned to a reference sequence. I want to be able to see the "gaps" between my contigs so I can amplify and Sanger-sequence these regions to close the circular genome.
Also, how do people usually deal with the inverted repeat in the chloroplast genome?
Any suggestions will be very much appreciated!