Packages / Debian 12 (Bookworm) / contrib/science / bcbio
Package: bcbio (1.2.9-2)
Maintainers:
External Resources:
Homepage: [github.com]
toolkit for analysing high-throughput sequencing data
Other Packages Related to bcbio:
dep: [python3] [any]
interactive high-level object-oriented language (default python3 version)
dep: [python3-bcbio]
library for analysing high-throughput sequencing data
rec: [bcftools]
genomic variant calling and manipulation of VCF/BCF files
rec: [bwa]
Burrows-Wheeler Aligner
rec: [cnvkit]
Copy number variant detection from targeted DNA sequencing
rec: [cufflinks]
Transcript assembly, differential expression and regulation for RNA-Seq
rec: [delly]
Structural variant discovery by read analysis
rec: [fastqc]
quality control for high throughput sequence data
rec: [freebayes]
Bayesian haplotype-based polymorphism discovery and genotyping
rec: [grabix]
wee tool for random access into BGZF files
rec: [libvcflib-tools]
C++ library for parsing and manipulating VCF files (tools)
rec: [macs]
Model-based Analysis of ChIP-Seq on short reads sequencers
rec: [pythonpy]
'python -c', with tab completion and shorthand
rec: [rna-star]
ultrafast universal RNA-seq aligner
rec: [hisat2]
graph-based alignment of short nucleotide reads to many genomes
rec: [sambamba]
tools for working with SAM/BAM data
rec: [samblaster]
marks duplicates, extracts discordant/split reads
rec: [samtools]
processing sequence alignments in SAM, BAM and CRAM formats
rec: [salmon]
wicked-fast transcript quantification from RNA-seq data
rec: [stringtie]
assemble short RNAseq reads to transcripts
rec: [subread]
toolkit for processing next-gen sequencing data
rec: [tabix]
generic indexer for TAB-delimited genome position files
rec: [umis]
tools for processing UMI RNA-tag data
rec: [varscan]
variant detection in next-generation sequencing data
rec: [wget]
retrieves files from the web
rec: [wham-align]
Wisconsin's High-Throughput Alignment Method
sug: [toil]
cross-platform workflow engine
sug: [cwltool]
Common Workflow Language reference implementation
sug: [kallisto]
near-optimal RNA-Seq quantification
sug: bcbio-doc
Package not available
sug: qualimap
Package not available
sug: [libglu1-mesa]
Mesa OpenGL utility library (GLU)
sug: tophat2
Package not available
sug: [tophat-recondition]
post-processor for TopHat unmapped reads
sug: [r-bioc-summarizedexperiment]
BioConductor assay container
sug: [r-cran-tidyverse]
Easily Install and Load the 'Tidyverse'
sug: [r-other-wasabi]
prepare Sailfish and Salmon output for downstream analysis using GNU R
Download bcbio
| Architecture | Package Size | Installed Size | Files |
|---|---|---|---|
| all | 75 KiB | 285 KiB | [list of files] |
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