SAMBLASTER：快速重复标记和结构变体读取提取
SAMBLASTER: fast duplicate marking and structural variant read extraction
摘要：
动机：Illumina DNA测序现在是原始基因组数据的主要来源，数据量正在迅速增长。生物信息学分析管道很难跟上步伐。这种管道中的一个常见瓶颈是需要多次读取、写入、排序和压缩大型BAM文件。结果：我们提出了SAMBLASTER，一种工具，减少了执行这种昂贵的操作的次数。SAMBLASTER旨在将读排序SAM文件中的重复标记为DNA比对器输出的管道后传递，然后将其压缩为BAM。此外，它可以同时将用于结构变异检测的不一致读段对和/或拆分读段映射输出到单独的文件中。作为对齐后传递，其自身的运行时开销可以忽略不计，同时显著降低了整体管道复杂性和运行时。作为一个独立的重复标记工具，它在速度和内存使用方面的表现明显优于PICARD或SAMBAMBA，同时达到几乎相同的结果。可用性：SAMBLASTER是开源C++代码，可从https://github.com/GregoryFaust/samblaster免费获得
英文摘要：
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times. Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results. Availability: SAMBLASTER is open source C++ code and freely available from https://github.com/GregoryFaust/samblaster
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
