- 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...
11 KB (1,395 words) - 09:07, 4 April 2025
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...
5 KB (366 words) - 22:25, 10 June 2025
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...
13 KB (1,061 words) - 23:05, 3 April 2025
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...
14 KB (1,100 words) - 13:02, 30 January 2024
Institute, and became widely known through its implementation within the SAMtools software suite. Each line consists of 5 (or optionally 6) tab-separated...
6 KB (575 words) - 02:25, 27 December 2023
bacteria Sustained Acoustic Medicine, a medical treatment for arthritis SAMtools (for Sequence Alignment Map), a data storage format for DNA sequencing...
7 KB (831 words) - 17:39, 2 May 2025
ISSN 1367-4803. PMC 6298042. PMID 30020420. "Description of A2M alignment format". SAMtools. Archived from the original on 2022-08-15. "soedinglab/hh-suite: reformat...
26 KB (2,148 words) - 14:45, 24 May 2025
generation sequencing (NGS) through the development of software such as the SAMtools NGS utilities, the Burrows–Wheeler aligner (BWA), MAQ, TreeSoft and TreeFam...
17 KB (727 words) - 23:44, 17 April 2025
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...
6 KB (506 words) - 13:30, 10 March 2025
PMC 3083090. PMID 21245279. "Htsjdk by Broad Institute". samtools.github.io. Retrieved 2018-10-14. "Samtools". www.htslib.org. Retrieved 2018-10-14. "JBrowse...
8 KB (577 words) - 00:51, 7 May 2025
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...
14 KB (1,495 words) - 03:34, 9 September 2024
Description format) and PIK image compressor, CRAM DNA compressor from SAMtools utilities, NVIDIA nvCOMP high speed compression library, Dropbox DivANS...
29 KB (3,719 words) - 06:30, 14 April 2025
supports multithreading for operations except listing of sequence names. SAMtools Li, Heng (March 1, 2011). "Tabix: fast retrieval of sequence features from...
2 KB (229 words) - 23:43, 17 April 2025
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...
25 KB (2,944 words) - 04:42, 22 May 2025
accepted by the convert2annovar.pl include the following: Variant Call Format Samtools genotype-calling pileup format Illumina export format from GenomeStudio...
30 KB (3,454 words) - 04:02, 12 December 2023
def samtoolsSort( bam : File ) -> <sorted : File> in Bash *{ sorted=sorted.bam samtools sort -m 2G $bam -o $sorted }* In this example a task samtoolsSort...
19 KB (1,834 words) - 07:27, 4 April 2025
libraries for scripting Linux, macOS, Windows GPL University of Ljubljana SAMtools Utilities for interacting with high-throughput sequencing data and alignments...
13 KB (158 words) - 16:13, 11 June 2025
Processing Subgroup (2009) (2009). "The Sequence alignment/map (SAM) format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352...
48 KB (1,505 words) - 07:28, 10 June 2025
similar to DNA variant calling and often employs the same tools (including SAMtools mpileup and GATK HaplotypeCaller) with adjustments to account for splicing...
87 KB (9,425 words) - 12:36, 10 June 2025
within Biopython. These wrappers include BLAST, Clustal, PhyML, EMBOSS and SAMtools. Users can subclass a generic wrapper class to add support for any other...
17 KB (1,811 words) - 13:54, 27 April 2025
Project Huffman coding http://public.tgen.org/sqz -Undeclared- CRAM (part of SAMtools) Highly efficient and tunable reference-based compression of sequence data...
18 KB (1,423 words) - 19:55, 18 June 2025
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...
120 KB (12,519 words) - 13:36, 25 January 2025
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...
28 KB (2,912 words) - 20:25, 6 April 2025
"Burrows–Wheeler Aligner". bio-bwa.sourceforge.net. Retrieved 18 October 2019. "SAMtools". samtools.sourceforge.net. Retrieved 18 October 2019. "TopHat". ccb.jhu.edu...
16 KB (1,468 words) - 18:16, 9 May 2025
(indels), and large structural variants. The read alignments are sorted using SAMtools, after which variant callers such as GATK are used to identify differences...
33 KB (3,896 words) - 20:21, 18 June 2025
RNA-Seq. The pipeline employs tools like Bowtie, TopHat, ArrayExpressHTS and SAMtools. Also, edgeR or DESeq to perform differential expression. MultiDE Myrna...
164 KB (20,394 words) - 21:36, 16 June 2025
Data Processing Subgroup (2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352...
16 KB (1,074 words) - 02:08, 1 December 2024
JointSNVMix MaCH Magnolia DCNN NeuSomatic NGSEP Pisces Platypus realSFS Reveel SAMtools SNVmix SOAPsnp SomaticSeq SomaticSniper Strelka VarDict VarScan Nielsen...
23 KB (3,217 words) - 11:01, 8 May 2025