Abstract: Disclosed herein include systems, machines, devices, and methods for single-pass methylation mapping. C-to-T converted sequence reads and G-to-A converted sequence reads generated from a sample subjected to a methylation assay can be mapped to a mapping reference sequence comprising a C-to-T converted reference sequence and a G-to-A converted reference sequence generated to a reference genome sequence. The counts of Cs and Ts of sequence reads mapped to each of one or more positions with Cs in the reference genome sequence can be used to determine whether the position is a methylated C or an unmethylated C in the sample.

Abstract: An iterative process may be implemented for incrementally aggregating available batches of sample data with previously available batches to perform sequencing analysis. Genomic variant call files associated with one or more samples may be received in batches from sequencing devices and aggregated for performing sequencing analysis. The aggregated genomic variant call files may be used to generate cohort files and census files that comprise summary information related to the genomic variant call files in each batch. The census data in census files may be aggregated into a global census file that includes summary genome variant data. Multi-sample variant call files may be generated based on the global census file, cohort files, and census files. The genomic variant call files may be processed using parallel processing at multiple compute nodes. The files may be further compressed and overlapping data may be efficiently stored in buffer positions.

Abstract: Disclosed herein include systems, devices, and methods for grouping sequence reads and collapsing families of sequence reads that originate from the same DNA molecules using UMIs.

Abstract: A database system performs hash join process for processing queries that join an inner and an outer database table. The hash join processes builds a hash table in memory for the inner table. The database system receives a limit on the memory for storing the hash table. The database system maximizes the number of partitions stored in memory for the hash table. If the hash table exceeds the limit of the memory while adding rows from the inner table, the database system selects a partition for spilling to a persistent storage. The partition selected for spilling to may be the largest partition or a partition larger than most of the partitions. The database system initializes the hash table to a number of partitions that is substantially equal to half of the total number of blocks that can be stored within the specified limit of memory for the hash table.

Abstract: Data of a columnar database is organized into extents. Each extent occupies contiguous storage on the disk. An extent stores database blocks of a column of a database table. The database system adds new database blocks of a column to the extents assigned to that column. When a request for adding a block to a table is received, the extent for the table and column combination is obtained and the block added to the extent. Prefetching strategies are used to retrieve database blocks in advance of an actual request. The rate of prefetching is determined per column. The rate of prefetching is adjusted based on the number of faults encountered for the column. Database blocks no longer needed in memory are pushed out. When a scan process is reading blocks, as soon as the block has been processed it is scheduled to be pushed out.

Abstract: Data of a columnar database is organized into extents. Each extent occupies contiguous storage on the disk. An extent stores database blocks of a column of a database table. The database system adds new database blocks of a column to the extents assigned to that column. When a request for adding a block to a table is received, the extent for the table and column combination is obtained and the block added to the extent. Prefetching strategies are used to retrieve database blocks in advance of an actual request. The rate of prefetching is determined per column. The rate of prefetching is adjusted based on the number of faults encountered for the column. Database blocks no longer needed in memory are pushed out. When a scan process is reading blocks, as soon as the block has been processed it is scheduled to be pushed out.

Abstract: Data of a columnar database is organized into extents. Each extent occupies contiguous storage on the disk. An extent stores database blocks of a column of a database table. The database system adds new database blocks of a column to the extents assigned to that column. When a request for adding a block to a table is received, the extent for the table and column combination is obtained and the block added to the extent. Prefetching strategies are used to retrieve database blocks in advance of an actual request. The rate of prefetching is determined per column. The rate of prefetching is adjusted based on the number of faults encountered for the column. Database blocks no longer needed in memory are pushed out. When a scan process is reading blocks, as soon as the block has been processed it is scheduled to be pushed out.

Abstract: A database system performs hash join process for processing queries that join an inner and an outer database table. The hash join processes builds a hash table in memory for the inner table. The database system receives a limit on the memory for storing the hash table. The database system maximizes the number of partitions stored in memory for the hash table. If the hash table exceeds the limit of the memory while adding rows from the inner table, the database system selects a partition for spilling to a persistent storage. The partition selected for spilling to may be the largest partition or a partition larger than most of the partitions. The database system initializes the hash table to a number of partitions that is substantially equal to half of the total number of blocks that can be stored within the specified limit of memory for the hash table.