Samtools view: - reformat, filter, or subsample SAM, BAM or CRAM

Metadata

Links

• bio.tools: SAMtools

EDAM Operations

• Filtering
• Sorting
• Visualisation
• Parsing
• Editing
• Formatting
• Indexing

EDAM Topics

• Sequence analysis
• Mapping
• Rare diseases
• Sequencing

Observed Tool Versions

Within GTN tutorials

1.20+galaxy3

• UseGalaxy.eu ⭐️
• UseGalaxy.fr ⭐️
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️

1.15.1+galaxy2

• UseGalaxy.eu ⭐️
• UseGalaxy.fr ⭐️
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️
• Galaxy@AuBi
• MISSISSIPPI

1.15.1+galaxy0

• UseGalaxy.eu ⭐️
• UseGalaxy.fr ⭐️
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️
• UseGalaxy.cz
• UseGalaxy.no

1.13+galaxy2

• UseGalaxy.eu ⭐️
• UseGalaxy.fr ⭐️
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️
• UseGalaxy.no

1.9+galaxy3

• UseGalaxy.eu ⭐️
• UseGalaxy.fr ⭐️
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️
• GalaxyTrakr
• UseGalaxy.no

1.9+galaxy2

• UseGalaxy.eu ⭐️
• UseGalaxy.fr ⭐️
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️
• UseGalaxy.no

1.9+galaxy1

• UseGalaxy.eu ⭐️
• UseGalaxy.fr ⭐️
• UseGalaxy.org (Main) ⭐️
• UseGalaxy.org.au ⭐️
• UseGalaxy.be
• UseGalaxy.no

Relevant Tutorials

• Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
• Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
• Introduction to Galaxy Analyses / NGS data logistics
• Transcriptomics / Reference-based RNA-Seq data analysis
• Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
• Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease
• Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
• Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC