trimmomatic
from the Usadel lab.
It's helpful to a create a shortcut so that you can call the command by typing trimmomatic
rather than remembering the more complicated java command line every time. You can do this by adding a line like this to your bash profile:
alias trimmomatic='java -jar /Users/name/local/bin/trimmomatic-0.XX.jar'
Replace the path with the path to the *.jar file and the XX with the version number.
The command line does not provide very detailed help, so keep the Manual (PDF) handy!
trimmomatic
is that is deals well with collapsing and trimming paired-end sequencing of fragments that are shorter than the read length, where the read extends into the adaptors at the end of each read.
In this PE mode, trimmomatic
will collapse these sequences to a single (and now unpaired) read, so that it will not be counted as sequencing of two independent DNA molecules This is important when analyzing sequences isolated from a mixed population.
The manual didn't exactly make it clear what adaptor sequences need to be included to get this trimming to work properly. So let's assume you have constructed a library with this format.
Adaptor1-Forward‑Sequenced-DNA‑Adaptor2-Forward gdtools RUNFILE
command to generate your trimming commands, this will re-combine all of the R1 and R2 sequences into two files that will no longer have the same number of sequences in them (so they are not suitable for input for paired-end mapping). You can use the -p
option to preserve the pairing in the output files (creating the normal 4 rather than 2 output files). Barrick Lab > ComputationList > ProtocolsTrimmomaticCommands