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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 ...
Raw PacBio subreads use the same convention but typically assign a placeholder base quality (Q0) to all bases in the read. [7] Oxford Nanopore Duplex reads, called using the dorado basecaller are typically stored in SAM/BAM format. After changing to a 16-bit internal quality representation, the reported base quality limit is q50 (S). [8]
Signed binary angle measurement. Black is traditional degrees representation, green is a BAM as a decimal number and red is hexadecimal 32-bit BAM. In this figure the 32-bit binary integers are interpreted as signed binary fixed-point values with scaling factor 2 −31, representing fractions between −1.0 (inclusive) and +1.0 (exclusive).
BEDTools: program allowing the manipulation of coordinate sets and the extraction of sequences from a BED file. [6] BEDOPS: a suite of tools for fast boolean operations on BED files. [8] BedTk: a faster alternative to BEDTools for a limited and specialized sub-set of operations. [9] covtobed: a tool to convert a BAM file into a BED coverage ...
Compressed Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence, initially devised by Markus Hsi-Yang Fritz et al. [1] CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file ...
Solid Converter PDF is document reconstruction software from Solid Documents which converts PDF files to editable formats. Originally released for the Microsoft Windows operating system, a Mac OS X version was released in 2010. The current versions are Solid Converter PDF 9.0 for Windows and Solid PDF to Word for Mac 2.1.