Everything about SAMtools
Tools for interacting with short DNA sequence read alignments
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. Both simple and advanced tools are provided, supporting complex tasks like variant calling and alignment viewing as well as sorting, indexing, data extraction and format conversion. SAM files can be very large, so compression is used to save space. SAM files are human-readable text files, and BAM files are simply their binary equivalent, whilst CRAM files are a restructured column-oriented binary container format. BAM files are typically compressed and more efficient for software to work with than SAM. SAMtools makes it possible to work directly with a compressed BAM file, without having to uncompress the whole file. Additionally, since the format for a SAM/BAM file is somewhat complex - containing reads, references, alignments, quality information, and user-specified annotations - SAMtools reduces the effort needed to use SAM/BAM files by hiding low-level details. Wikipedia →
🧠Start here: a 6-step reading path
- Read the overview: SAMtoolsA 5-minute orientation
- Read the landmark paper: The Sequence Alignment/Map format and SAMtoolsCited 61,839 times
- Go sideways: BGZFA closely related topic
- Go sideways: BAM (file format)A closely related topic
đź“– Definitions
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🗂️ The subject at a glance
🏆 Landmark papers (most cited)
The Sequence Alignment/Map format and SAMtools
Twelve years of SAMtools and BCFtools
bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby
Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples
Optimization of SAMtools sorting using OpenMP tasks
bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
7bgzf: Replacing samtools bgzip deflation for archiving and real-time compression
đź“š Books worth reading
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đź”— Related topics
- BGZF Blocked GNU Zip Format (BGZF) is a variant of gzip file format that uses block compression, a method that compresses data in independent blocks of content—each…
- BAM (file format) The BAM file format (which stands for Binary Alignment Map) is the lossless, compressed binary representation of a Sequence Alignment Map file. It is compressed…
- SAM (file format) Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and…
- CRAM (file format) Compressed Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence…
- Variant Call Format The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was…
- Tabix Tabix is a free software utility for indexing TAB-delimited genome position files. It is commonly used in bioinformatics analysis to index large genomic…
- Pileup format Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of…
- UGENE UGENE is computer software for bioinformatics. It helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple…