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Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker et al. [1] It was developed when the 1000 Genomes Project wanted to move away from the MAQ mapper format and decided to design a new format.
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). [5] To view a list of sequencing and analysis tools that work with SAM/BAM click here.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li.
^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality $ (dollar) marks the end of a read segment * (asterisk) is a placeholder for a deleted base in a multiple basepair deletion that was mentioned in a previous line by the -[0-9] + [ACGTNacgtn] + notation
FastQC is a quality control tool for high-throughput sequence data (Babraham Institute) and is developed in Java. Import of data is possible from FastQ files, BAM or SAM format. This tool provides an overview to inform about problematic areas, summary graphs and tables to rapid assessment of data.
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Indexes the genome with a k-mer lookup table with full sensitivity up to an adjustable number of mismatches. It is best for mapping 15-60 bp sequences to a genome. No No Yes No, multiple processes per search 2003 QPalma Can use quality scores, intron lengths, and computation splice site predictions to perform and performs an unbiased alignment.
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