套件：bcbio（1.2.5-1） [contrib]
toolkit for analysing high-throughput sequencing data
This package installs the command line tools of the bcbio-nextgen toolkit implementing best-practice pipelines for fully automated high throughput sequencing analysis.
A high-level configuration file specifies inputs and analysis parameters to drive a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The project contributes a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
This package builds and having it in Debian unstable helps the Debian developers to synchronize their efforts. But unless a series of external dependencies are not installed manually, the functionality of bcbio in Debian is only a shadow of itself. Please use the official distribution of bcbio for the time being, which means "use conda". The TODO file in the Debian directory should give an overview on progress for Debian packaging.
其他與 bcbio 有關的套件
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-bcbio
- library for analysing high-throughput sequencing data
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- rec: bcftools
- genomic variant calling and manipulation of VCF/BCF files
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- rec: cnvkit
- Copy number variant detection from targeted DNA sequencing
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- rec: cufflinks
- Transcript assembly, differential expression and regulation for RNA-Seq
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- rec: delly
- Structural variant discovery by read analysis
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- rec: fastqc
- quality control for high throughput sequence data
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- rec: freebayes
- Bayesian haplotype-based polymorphism discovery and genotyping
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- rec: grabix
- wee tool for random access into BGZF files
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- rec: hisat2
- graph-based alignment of short nucleotide reads to many genomes
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- rec: libvcflib-tools
- C++ library for parsing and manipulating VCF files (tools)
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- rec: macs
- Model-based Analysis of ChIP-Seq on short reads sequencers
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- rec: pythonpy
- 'python -c', with tab completion and shorthand
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- rec: rna-star
- ultrafast universal RNA-seq aligner
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- rec: salmon
- wicked-fast transcript quantification from RNA-seq data
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- rec: sambamba
- tools for working with SAM/BAM data
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- rec: samblaster
- marks duplicates, extracts discordant/split reads
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- rec: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- rec: stringtie
- assemble short RNAseq reads to transcripts
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- rec: subread
- toolkit for processing next-gen sequencing data
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- rec: tabix
- generic indexer for TAB-delimited genome position files
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- rec: umis
- tools for processing UMI RNA-tag data
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- rec: varscan
- variant detection in next-generation sequencing data
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- rec: wget
- retrieves files from the web
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- rec: wham-align
- Wisconsin's High-Throughput Alignment Method
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- sug: bcbio-doc
- 套件暫時不可用
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- sug: cwltool
- Common Workflow Language reference implementation
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- sug: kallisto
- near-optimal RNA-Seq quantification
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- sug: libglu1-mesa
- Mesa OpenGL utility library (GLU)
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- sug: qualimap
- 套件暫時不可用
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- sug: r-other-wasabi
- prepare Sailfish and Salmon output for downstream analysis using GNU R
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- sug: toil
- cross-platform workflow engine
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- sug: tophat-recondition
- post-processor for TopHat unmapped reads
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- sug: tophat2
- 套件暫時不可用