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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 bitmap was contained in 3 bytes for Commodore 1541 format (single-sided) disks because it had 17 to 20 sectors per track (note 3 bytes can hold at least 20 bits). [6] Similarly, the Commodore 1571 used 3 bytes for the bitmap of each track, but the BAM was twice the size because there were twice as many tracks when formatted as double-sided ...
Uses a short kmers to rapidly index genome; no size or scaffold count limit. Higher sensitivity and specificity than Burrows–Wheeler aligners, with similar or greater speed. Performs affine-transform-optimized global alignment, which is slower but more accurate than Smith-Waterman. Handles Illumina, 454, PacBio, Sanger, and Ion Torrent data.
PacBio's (PACB) latest acquisition is expected to deliver the most advanced blend of sequencing solutions to transform the genomics landscape.
The input can be SAM, BAM, FASTA, BED files or Chromosome size file (two-column, plain text file). Visualization can be performed by genome browsers like UCSC, IGB and IGV. However, R scripts can also be used for visualization. SAMStat [15] identifies problems and reports several statistics at different phases of the process. This tool ...
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]