79 lines
2.5 KiB
Markdown
79 lines
2.5 KiB
Markdown
# FastDup
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Identifies duplicate reads. This tool locates and tags duplicate reads in a coordinate ordered SAM or BAM file.
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Use the same algorithm as picard MarkDuplicates and output identical results.
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Use spdlog as log tool and the default level is 'info'.
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### Features
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* Fast - with the same number of threads `FastDup` is ~8X faster than GATK MarkDuplicatesSpark.
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And `FastDup` achives ~20X performance improvement than Picard MarkDuplicates.
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* Generate identical outputs compared to Picard MarkDuplicates.
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* The same detailed metrics data witch Picard MarkDuplicates.
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* All data processed in memory and low-memory footprint even for large input files.
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### Limitations
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* Although `FastDup` can detecte all the same duplicates as Picard MarkDuplicates. They may mark
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different reads as duplicates because the reads sort algorithm in Picard MarkDuplicates is unstable.
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Considering there are 2 reads(A, B and A is in front of B in file) in a duplicate group and they
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have the same score, Picard Markduplicates may mark A as duplicate because B may be in front of A
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after sorting. While `FastDup` use stable sort algorithm and always mark B as duplicate.
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* In optical duplicates detection, Picard Markduplicates use short (int16_t) as data type in parsing
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tile/region, x coordinate and y coordinate from a read name, which may data overflow as these integers
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may exceed the range of short type. `FastDup` fixes this bug. But for consistency with Picard Markduplicates,
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we keep this bug in source codes. Just change the data type in PhysicalLocation struct in read_ends.h file
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to fix this bug.
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* `FastDup` use the data characteristics in coordinate ordered SAM/BAM files to improve the performance of
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detecting duplicates, thus the input should be ordered by coordinate in advance.
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## Requirements
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### Build tools
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* autoconf (for htslib)
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* cmake
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* c++17 (gcc >= 8.1 or clang >= 7 should work.)
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### Libraries needed
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* zlib
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* libbz2
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* liblzma
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* libcurl
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* libdeflate (optional)
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## Install
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Download a distribution tarball `FastDup.tar.gz` or clone the source codes from github.
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```bash
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# build htslib
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cd FastDup/ext/htslib
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autoreconf -i
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./configure
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make
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# build FastDup
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cd FastDup
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mkdir build && cd build
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cmake .. -DCMAKE_BUILD_TYPE=Release
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make
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```
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The generated binary fastdup will be in the build/bin folder.
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## Usage
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Get help
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```bash
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./fastdup --help
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```
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Mark duplicates on an input BAM file using 8 threads
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```bash
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./fastdup --input in_test.bam --output out_md.bam --metrics stats.txt --num-threads 8
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``` |