A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data <s> Auxiliary Tools. <s> Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. ::: ::: Availability: http://samtools.sourceforge.net ::: ::: Contact: [email protected] <s> BIB001 </s> A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data <s> Auxiliary Tools. <s> The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time, which increases linearly at an average speed of 87 million reads per 10 minutes. FastUniq is freely available at http://sourceforge.net/projects/fastuniq/. <s> BIB002
Some auxiliary tools have been developed to filter aligned reads to ensure higher quality data for downstream analyses. PCR amplification can introduce duplicate reads of paired-end reads in sequencing data. These duplicate reads can influence the depth of the mapped reads and downstream analyses. For example, if a variant is detected in duplicate reads, the proportion of reads containing a variant could pass the threshold needed for variant calling, thus calling a falsely positive variant. Therefore, removing duplicate reads is a crucial step in accurately representing the sequencing depth during downstream analyses. Several tools have been developed to detect PCR duplicates including Picard (http://picard.sourceforge.net./), FastUniq BIB002 , and SAMtools BIB001 . SAMtools rmdup finds reads that start and end at the same position, find the read with the highest quality score, and mark the rest of the duplicates for removal. Picard finds identical 5 positions for both reads in a mate pair and marks them as duplicates. In contrast, FastUniq takes a de novo approach to quickly identify PCR duplicates. FastUniq imports all reads, sorts them according to their location, and then marks duplicates. This allows FastUniq not to require complete genome sequences as prerequisites. Due to the different algorithms each of these tools use, these tools can remove PCR duplicates individually or in combination.