Running bowtie 2.0.2 with the following invocation:
bowtie2 \ --time -p 48 --mm \ --phred33 --sensitive --end-to-end \ -U reads.fastq \ -x ~/data/reference/genome \ --al reads.matched.fastq \ --un reads.unmatched.fastq \ 2> bowtie2.log \ | samtools view -Sb - > reads.mapped.bam
Input reads are long (~500-10000bp).
Both --al and --un fastq outputs are malformed with the seq header occasionally being inserted at the end of the previous read's qual line, rather than on a new line. Also, some quality lines appear to be truncated.