![]() Trimming reads and removing adapter sequences Sometimes Illumina adapter sequences are still present in some reads because adapters can form adapter dimers and then one of them gets sequenced or if a DNA fragment is shorter than the read length, the sequencer continues to “read-through” into the adapter at the end of the DNA fragment. Trimmomatic is far above average for as far as programs go, most will not have a user manual, may not have been updated since originally published, etc. Trimmomatic's home pagecan be found at this link which includes links to the paper discussing the program, and a user manual. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Trimmomatic uses two strategies for adapter trimming: Palindrome and Simple With 'simple' trimming, each adapter sequence is tested against the reads, and if a sufficiently accurate match is detected, the read is clipped appropriately.
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