I have some mixed genome sequence data of an insect. The insect contains 1 known and probable some unknown symbionts. Could someone please suggest me how can I identify the unknown symbionts if they exist in insect?
Xabier Vázquez Campos
Did you do the sequencing? If so you can map the reads against the genome and search for islands or contigs with very different coverage
You can also redo the genome assembly trying to delimitate the reads to be used in each assembly based on the kmer frequency. You can do that with the velvet stats output file in R generating a graph:
>R --no-save --no-restore
>library(plotrix)
>data weighted.hist(data$short1_cov, data$lgth, breaks=0:50)
>dev.off()
Change the "breaks" parameter to change the range of your kmer coverage axis
0 votes
0 thanks
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology
More Ashmit Singh's questions See All
Similar questions and discussions