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Tools for interacting with short DNA sequence read alignments
- SAMtools reduces the effort needed to use SAM/BAM files by hiding low-level details. As third-party projects were trying to use code from SAMtools despite
SAMtools
File format for gene sequences
PMID 19505943. Edmunds, Scott (2021-02-17). "Play it again, SAMtools. Q&A with the SAMtools team on 12 years of providing bioinformatics "glue"". GigaScience
SAM_(file_format)
Raw data of genome sequencing
analysis tools that work with SAM/BAM click here. FASTQ format SAM format SAMtools CRAM format List of file formats for molecular biology Compression of Genomic
BAM_(file_format)
File format for genomic variation data
with the VCF format in 2011, and BCFtools, which was included as part of SAMtools until being split into an independent package in 2014. The standard is
Variant_Call_Format
File format for block-based Gzip compression
processing. The format was developed as part of SAM/BAM specification and SAMtools. It is a core component of the common BAM format (the binary version of
BGZF
File format for sequence data
Institute, and became widely known through its implementation within the SAMtools software suite. Each line consists of 5 (or optionally 6) tab-separated
Pileup_format
Bioinformatician
generation sequencing (NGS) through the development of software such as the SAMtools NGS utilities, the Burrows–Wheeler aligner (BWA), MAQ, TreeSoft and TreeFam
Heng_Li
File format for DNA or protein sequences
May 2019. Retrieved 22 May 2019. "Description of A2M alignment format". SAMtools. Archived from the original on 2022-08-15. "soedinglab/hh-suite: reformat
FASTA_format
File format for sequence alignments
PMC 3083090. PMID 21245279. "Htsjdk by Broad Institute". samtools.github.io. Retrieved 2018-10-14. "Samtools". www.htslib.org. Retrieved 2018-10-14. "JBrowse
CRAM_(file_format)
Topics referred to by the same term
bacteria Sustained Acoustic Medicine, a medical treatment for arthritis SAMtools (for Sequence Alignment Map), a data storage format for DNA sequencing
Sam
File format used for genomes
Retrieved 2 October 2019. "The Browser Extensible Data (BED) format" (PDF). samtools.github.io. "GA4GH BED v1.0: A formal standard sets ground rules for genomic
BED_(file_format)
Entropy coding methods
Description format) and PIK image compressor, CRAM DNA compressor from SAMtools utilities, NVIDIA nvCOMP high speed compression library, Dropbox DivANS
Asymmetric_numeral_systems
poi 0.13.3 4 Bio gem Software generator for Ruby 1.36 5 Bio samtools Binder of samtools for Ruby 2.1.0 6 t2 server Support for interacting with the taverna
BioRuby
Open-source workflow language
def samtoolsSort( bam : File ) -> <sorted : File> in Bash *{ sorted=sorted.bam samtools sort -m 2G $bam -o $sorted }* In this example a task samtoolsSort
Cuneiform (programming language)
Cuneiform_(programming_language)
Computer software for bioinformatics
"Burrows–Wheeler Aligner". bio-bwa.sourceforge.net. Retrieved 18 October 2019. "SAMtools". samtools.sourceforge.net. Retrieved 18 October 2019. "TopHat". ccb.jhu.edu
UGENE
Bioinformatics software utility
supports multithreading for operations except listing of sequence names. SAMtools Li, Heng (March 1, 2011). "Tabix: fast retrieval of sequence features from
Tabix
libraries for scripting Linux, macOS, Windows GPL University of Ljubljana SAMtools Utilities for interacting with high-throughput sequencing data and alignments
List of open-source bioinformatics software
List_of_open-source_bioinformatics_software
Bioinformatics software
accepted by the convert2annovar.pl include the following: Variant Call Format Samtools genotype-calling pileup format Illumina export format from GenomeStudio
ANNOVAR
Lab technique in cellular biology
similar to DNA variant calling and often employs the same tools (including SAMtools mpileup and GATK HaplotypeCaller) with adjustments to account for splicing
RNA-Seq
Processing Subgroup (2009) (2009). "The Sequence alignment/map (SAM) format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352
List of filename extensions (M–R)
List_of_filename_extensions_(M–R)
Collection of open-source Python software tools for computational biology
included command-line wrappers for tools such as BLAST, Clustal, EMBOSS, and SAMtools. This option allowed users to run external tool commands from within the
Biopython
Methods of compressing data tailored specifically for genomic data
Project Huffman coding http://public.tgen.org/sqz -Undeclared- CRAM (part of SAMtools) Highly efficient and tunable reference-based compression of sequence data
Compression of genomic sequencing data
Compression_of_genomic_sequencing_data
Open source column-oriented relational database management system
set of SQL UDFs for working with DNA data. The module uses the popular SAMtools library. MonetDB/RDF is a SPARQL-based extension for working with linked
MonetDB
Study of RNA transcripts
Abecasis G, Durbin R (August 2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–9. doi:10.1093/bioinformatics/btp352. PMC 2723002
Transcriptomics_technologies
Method of DNA sequence reconstruction
This is an assembly tool that runs on the command line. Samtools Alignment analysis https://samtools.github.io This is useful post-assembly. It can generate
Sequence_assembly
Monthly scientific journal established 1994
Information Network Software BLAST Bowtie Clustal EMBOSS HMMER MUSCLE PANGOLIN SAMtools SOAP suite TopHat Other Server: ExPASy Rosalind (education platform) Institutions
Journal of Computational Biology
Journal_of_Computational_Biology
JointSNVMix MaCH Magnolia DCNN NeuSomatic NGSEP Pisces Platypus realSFS Reveel SAMtools SNVmix SOAPsnp SomaticSeq SomaticSniper Strelka VarDict VarScan Nielsen
SNV_calling_from_NGS_data
Identification and study of genomic sequences
(indels), and large structural variants. The read alignments are sorted using SAMtools, after which variant callers such as GATK are used to identify differences
Sequence_analysis
Portuguese researcher
Data Processing Subgroup (2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352
Gonçalo_Abecasis
RNA-Seq. The pipeline employs tools like Bowtie, TopHat, ArrayExpressHTS and SAMtools. Also, edgeR or DESeq to perform differential expression. MultiDE Myrna
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
SAMTOOLS
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