Add filter mlc parameter

Added

• 2 parameter for filter molecule: by number of reads and by length
• Add log data to summary.inf

MDUP first release

Developed by BioTuring (www.bioturing.com), mdup is a tool that preprocesses cloud-read data (read has barcode). mdup will:

• Removes duplicate reads, removes not primary reads, secondary alignment, unmapped reads.
• Detects molecule by clustering reads have same barcode into group.
• Gets stats about sequencing and GEM performance.

Two reads are considered duplicate if they share the same mapped position, mapped target, cigar, mate info (if paired-end).

mdup takes a BAM file as input, the Bam file must be sorted by coordinate and be indexed. We recommend using BWA to align cloud-reads to a referenece. All alignment records must have BX:Z: tag presented for barcode.

mdup will generate some files in output directory:

• output.bam : new BAM file after removing unneeded reads.
• molecule.tsv : all molecule detected info.
• summary.inf : stats about sequencing and GEM performance.
• plot.html : plots of some metrics of stats.