Sequence Analysis and Management (SAM) | Scientific Operations
Sequence Analysis and Management (SAM)
Sanger Institute, Genome Research Limited
Our Research and Approach
SAM contributes to various software packages for processing DNA sequence data, including samtools, htslib, biobambam and the Staden package. We also submit raw sequencing data to the EBI on behalf of the research groups.
Gap5 is a DNA sequence assembly visualiser and editing tool. It permits low level base by base editing as well as larger scale contig rearrangements such as complementing, joining and breaking apart contigs.
Input can be from CAF, ACE or more typically SAM, BAM and CRAM file formats.
Many high profile projects such as the Cancer Genome and 1000 Genomes projects need quality assemblies for downstream analysis using 2nd and 3rd generation sequencing data. Efficient bioinformatics tools in processing and analysis of large quantities of genomic data play crucial roles in producing high quality assemblies as well as variation detection. The High Performance Assembly Group (HPAG), headed by Zemin Ning, develops algorithms and software tools for genome analysis. Currently the team is also involved in data processing and quality evaluation of Oxford Nanopore sequencing technology.
The SAM team is responsible for archival of the data produced by NPG to external repositories, typically the EGA, ENA or ArrayExpress at the EBI. They also create and maintain tools which are essential components of our analysis pipelines.