Can Bowtie 0.12.7 handle Sanger / Illumina 1.9 ?

[nkline]

Hello. I have a user that needs to use Bowtie 0.12.7 (Yeah, old version. Don't ask.) but the quality score format of our FASTQ files is Sanger / Illumina 1.9.

According to https://en.wikipedia.org/wiki/FASTQ_format#Encoding , Illumina 1.8+ introduces a 41st score (letter "J"). And according to that article:

various scripts and tools break when they encounter data with quality values larger than 40

With that in mind, I see this version of Bowtie defaults to:

--phred33-quals    input quals are Phred+33 (default)

So my questions are:

1. Will Bowtie 0.12.7 know how to handle the 41st score (letter "J")?

2. If not, where can I find a command-line version of a FASTQ Groomer, like the one in Galaxy?

I appreciate your help.

[GenoMax]

For reference cross-posted: https://www.biostars.org/p/180855/