Hello!

I need to make contigs from the Ion Torrent data. This is a microbial genome fragment library. It supposed to be a set of 400 bp read. Due to quality reasons (I used FastQC to check) the reads are kind of good for the first 170-200bp. Our core sequencing facility releases the data as *.FASTQ files and the adaptors are supposed to be trimmed. 
I am not very experienced with NGS data analysis. The only program I used to clean my date was Trimmomatic but at that time I worked with Illumina reads.  
Could you suggest me something like Trimmomatic for my Ion-torrent data, please?

Thanks for your tips.
Optimal would be to use the ubam file straight from the sequencing machine with Spades assembler. You lose valuable information (that Spades utilizes) when you convert the ubam files to fastq.