Hi everyone,
I will be performing de novo and reference guided assembly of mitochondrial genomes using Geneious, and have a question regarding the minimum recommended read length to trim my reads to.
The libraries I have are Nextera XT prepared from purified organellar DNA (~450 kb genome), paired-end sequenced on MiSeq V3 with 300 bp reads. I am using Trimmomatic to trim my reads, and I notice that after quality trimming (without specifying a min length) that some of the reads are very short.
I am wondering what a good minimum length for trimming would be. I tried trimming to a min length of 250 bp, but that removes a lot of reads and seems too stringent. I am thinking a min length of 100-150 bp may be better.
Any suggestions?
I will be performing de novo and reference guided assembly of mitochondrial genomes using Geneious, and have a question regarding the minimum recommended read length to trim my reads to.
The libraries I have are Nextera XT prepared from purified organellar DNA (~450 kb genome), paired-end sequenced on MiSeq V3 with 300 bp reads. I am using Trimmomatic to trim my reads, and I notice that after quality trimming (without specifying a min length) that some of the reads are very short.
I am wondering what a good minimum length for trimming would be. I tried trimming to a min length of 250 bp, but that removes a lot of reads and seems too stringent. I am thinking a min length of 100-150 bp may be better.
Any suggestions?
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