- samtools-0.1.18 or 0.1.19 required samtools page Tested on 0.1.18
- python2.7 anaconda page Tested on 2.7.7
- GNU-coreutils gzip,sed,cut,grep etc. Standard on Ubuntu 12.04+.
Run python nudup.py -h for latest usage.
usage: nudup.py [-2] [-f INDEX.fq|READ.fq] [-o OUT_PREFIX] [-s START]
[-l LENGTH] [-v] [-h]
IN.sam|IN.bam
Marks/removes PCR introduced duplicate molecules based on the molecular tagging
technology used in NuGEN products.
For SINGLE END reads, duplicates are marked if they fulfill the following
criteria: a) start at the same genomic coordinate b) have the same strand
orientation c) have the same molecular tag sequence. The read with the
highest mapping quality is kept as the non-duplicate read.
For PAIRED END reads, duplicates are marked if they fulfill the following
criteria: a) start at the same genomic coordinate b) have the same template
length c) have the same molecular tag sequence. The read pair with the highest
mapping quality is kept as the non-duplicate read.
Here are the two cases for running this tool:
- CASE 1 (Standard): User supplies two input files,
1) SAM/BAM file that a) ends with .sam or .bam extension b) contains unique
alignments only
2) FASTQ file (ie: the Index FASTQ) that contains the molecular tag sequence
for each read name in the corresponding SAM/BAM file as either a) the read
sequence or b) in the FASTQ entry header name. If the index FASTQ read
length is 6, 8, 12, 14, or 18nt long as expected for NuGEN products, the
molecular tag sequence to be extracted from the read according to -s and -l
parameters, otherwise the molecular tag will be extracted from the header
of the FASTQ entry.
- CASE 2 (Runtime Optimized): User supplies only one input file,
1) SAM/BAM file that a) ends with .sam or .bam extension b) contains unique
alignments only c) is sorted d) has a fixed length sequence containing the
molecular tag appended to each read name.
Author: Anand Patel
Contact: NuGEN Technologies Inc., techserv@nugen.com
Input:
IN.sam|IN.bam input sorted/unsorted SAM/BAM containing only unique
alignments (sorted required for case 2 detailed above)
Options:
-2, --paired-end use paired end deduping with template. SAM/BAM
alignment must contain paired end reads. Degenerate
read pairs (alignments for one read of pair) will be
discarded.
-f INDEX.fq|READ.fq FASTQ file containing the molecular tag sequence for
each read name in the corresponding SAM/BAM file
(required only for CASE 1 detailed above)
-o OUT_PREFIX, --out OUT_PREFIX
prefix of output file paths for sorted BAMs (default
will create prefix.sorted.markdup.bam,
prefix.sorted.dedup.bam, prefix_dup_log.txt)
-s START, --start START
position in index read where molecular tag sequence
begins. This should be a 1-based value that counts in
from the 3' END of the read. (default = 6)
-l LENGTH, --length LENGTH
length of molecular tag sequence (default = 6)
-v, --version show program's version number and exit
-h, --help show this help message and exit
For questions, contact NuGEN Technologies Technical Support techserv@nugen.com