Differences from Juicer 1.5.6:

• bwa mem –SP5M paired end mode; most recent BWA release 0.7.17
• nofrag default
• no short end read alignment anymore
• alignonly, mergeonly, deduponly stages added
• simplification of chimeric_blacklist in terms of output stem
• chimeric_blacklist producing partition of reads into bams: - alignable.bam with duplicates marked - collisions.bam (those two ideally ENCODE product that one can download) - collisions_low_mapq.bam - unmapped.bam - mapq0.bam
• mitochondria no longer treated as a special case
• collisions now include contigs as well (blacklist instead of whitelist) The merged_nodups file still appears as part of the pipeline. To recover merged_nodups from alignable.bam produced by ENCODE (for example), use the bamtotxt.sh script