streammd: fast low-memory duplicate marking using a Bloom filter

被引：1
|
作者：
Leonard, Conrad [1 ,2 ]
机构：
[1] QIMR Berghofer Med Res Inst, Dept Genome Informat, Herston, Qld 4006, Australia
[2] QIMR Berghofer Med Res Inst, Dept Genome Informat, 300 Herston Rd, Herston, Qld 4006, Australia
来源：
BIOINFORMATICS | 2023年 / 39卷 / 04期
关键词：
D O I：
10.1093/bioinformatics/btad181
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Identification of duplicate templates is a common preprocessing step in bulk sequence analysis; for large libraries, this can be resource intensive. Here, we present streammd: a fast, memory-efficient, single-pass duplicate marker operating on the principle of a Bloom filter. streammd closely reproduces outputs from Picard MarkDuplicates while being substantially faster, and requires much less memory than SAMBLASTER.Availability and implementationstreammd is a C++ program available from GitHub under the MIT license.
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页数：3
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