I have data from a 2x150 Miseq run but I have noticed that the read lengths vary quite a lot. They range from 35 to 151 bp. I am interested in assembling these data with BWA or BOWTIE2 and I would like to know whether this is would be a problem and if not why? Thanks
Looks like the adpater/primer sequences and low quality ends have been trimmed out this data. Please ask the sequencing company though. Or may be you can use FASTQC or FASTX tools to view the quality of the reads and other read parameters. BWA and Bowtie2 are the mapping softwares, these packages can only map the reads on a reference genome. You are doing denovo assembly? May be one could try velvet or SoapDenovo for de-novo assembly.