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.