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Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4]
samtools view -h -b sample_sorted.bam "chr1:10-13" > tiny_sorted.bam. Extract the same reads as above, but instead of displaying them, writes them to a new bam file, tiny_sorted.bam. The -b option makes the output compressed and the -h option causes the SAM headers to be output also.
The SAM format consists of a header and an alignment section. [1] The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is ...
The preferred data format for files submitted to the SRA is the BAM format, which is capable of storing both aligned and unaligned reads. [6] Internally the SRA relies on the NCBI SRA Toolkit, used at all three INSDC member databases, to provide flexible data compression, API access and conversion to other formats such as FASTQ. [5]
Utilities for interacting with high-throughput sequencing data and alignments in sam/bam format Unix/Linux: MIT: Collaborative project SOAP Suite: Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data Unix/Linux, macOS: GPL: BGI: Staden Package
PacBio's (PACB) latest acquisition is expected to deliver the most advanced blend of sequencing solutions to transform the genomics landscape.
In the bitmap of any format, a 1 bit indicated the block was available (free), while a 0 bit indicated the block was not available (used), and the bitmap data was stored low-byte first. So the first byte held a map for blocks 0 to 7, the second byte held a map for blocks 8 to 15, and so on.
The output from this step, that is, the aligned reads, are stored in compatible file formats known as SAM, which contains information about the reference genome as well as individual reads. Alternatively, BAM file formats are preferred as they use much less desk or storage space.
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