It is not clear-cut trimming poly-A tails is beneficial, are you certain you need to trim the poly-A tail? As Jason pointed, many short read mappers won't be affected by poly-A tails. For assembly, it may help discern splice variants (see comment on MIRA's manual).

There is a tool available on Github for removing PolyA, PolyT, PolyC, PolyG

https://github.com/haploxer/after

• Automatic Filtering, Trimming, and Error Removing for fastq data
• Currently it supports Illumina 1.8 or newer format
• AFTER can simply go through all fastq files in a folder and then output a good folder and a bad folder, which contains good reads and bad reads of each fastq file

Besides remove PolyX, it also can do:

• Trim reads at front and tail according to bad per base sequence content
• Detect and eliminate bubble artifact caused by sequencer due to fluid dynamics issue
• Filter low-quality reads

You can use bbduk from the bbmap suite. Just create a polyA.fa (e.g. >polyA\nAAAAAAAAAAAAA) and zip it into the bbmap resources folder; run then bbduk with ref=resources/polyA.fa.gz. Maybe it is necessary to add a polyT sequence into your fasta.

I'm quite sure you can add the sequences to the adapter-file of trim_galore likewise.

Cheers,
Michael

Hello,

You can also try UrQt.

It performs poly-N trimming as well as quality trimming, searching for the best larger fragment in the whole read. It has a high percentage of base conservation. It is pretty effective.