Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate. BAM is in compressed BGZF format.
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| - Binary Alignment Map (en)
- Binary Alignment Map (fr)
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| - Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate. BAM is in compressed BGZF format. (en)
- Le format cartographie d'alignement binaire, binary alignment map (BAM) est constitué de données brutes complètes sur le séquençage génomique ; il s'agit de la représentation binaire compressée sans perte du format SAM. La compression utilisée est le format BGZF. Les fichiers BAM peuvent être générés directement par les programmes d'alignement ou par . (fr)
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| - Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate. BAM is in compressed BGZF format. The structure of BAM files include a header section and an alignment section:
* Header—The sample name, sample length, and alignment method are all included in this section. The alignments section contains alignments that are linked to specific information in the header section.
* Alignments—The read name, read sequence, read quality, alignment information, and custom tags are all included in this file. The chromosome, start coordinate, alignment quality, and match descriptor string are all included in the read name.
* Alignment Section includes the following:
* Read Group (RG)
* Barcode Tag (BC)
* Single-end alignment quality (SM)
* Paired-end alignment quality (AS)
* Edit distance tag (NM)
* Amplicon name tag (XN) Bam format uses 0-based coordinate system, where as SAM uses 1-based coordinate system. BAM can represent values in the range [−2^31 , 2^32). To view a list of sequencing and analysis tools that work with SAM/BAM click here. (en)
- Le format cartographie d'alignement binaire, binary alignment map (BAM) est constitué de données brutes complètes sur le séquençage génomique ; il s'agit de la représentation binaire compressée sans perte du format SAM. La compression utilisée est le format BGZF. Les fichiers BAM peuvent être générés directement par les programmes d'alignement ou par . Les fichiers BAM possèdent la même structure que les fichiers SAM. Du fait de leur taille réduite, les fichiers BAM sont plus facilement lisibles par les programmes dédiés au séquençage à haut débit. Il existe par exemple des librairies pour lire les fichiers BAM en Python et en R. Les fichiers BAM triés peuvent être indexés au travers d'un fichier BAI accompagnant, qui sert de table des matières au fichier BAM et permet d’accéder directement des parties spécifiques du fichier concerné (par exemple, une coordonnée chromosomique particulière), ce qui accélère grandement l'accès aux données. Certains logiciels comme , et requièrent un index pour lire les fichiers BAM. (fr)
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