Hi everyone
I recently used the clc genome finishing module autojoin tool to assemble my contigs. the tool reduced the number of contigs i had from 170 to 30, i also found that 1 of the contigs spanned a plasmid which was expected. i mapped reads to my joined contigs and had 94% of my reads mapping to the assembled contigs. i wish to know if there is a method for checking the quality of assembling my contigs ?? as i wish to know whether what i did to join contigs was correct
In order to assemble my contigs. I firstly used the join contigs tool which joined about 11 contigs, then i took the data and used the map contigs to a reference ( i have a reference thats similer to my contigs, this joined about 121 contigs and then i used map long reads to contigs tool and this joined 2 contigs.
just an added note: i am using Iontorrant PGM 400bp kit
thanks
I recently used the clc genome finishing module autojoin tool to assemble my contigs. the tool reduced the number of contigs i had from 170 to 30, i also found that 1 of the contigs spanned a plasmid which was expected. i mapped reads to my joined contigs and had 94% of my reads mapping to the assembled contigs. i wish to know if there is a method for checking the quality of assembling my contigs ?? as i wish to know whether what i did to join contigs was correct
In order to assemble my contigs. I firstly used the join contigs tool which joined about 11 contigs, then i took the data and used the map contigs to a reference ( i have a reference thats similer to my contigs, this joined about 121 contigs and then i used map long reads to contigs tool and this joined 2 contigs.
just an added note: i am using Iontorrant PGM 400bp kit
thanks
Comment