Paketti: bcbio (1.2.5-1) [contrib]

[ Source: bcbio  ]

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.

Muut pakettiin bcbio liittyvät paketit

• dep: python3

  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: 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: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• 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: salmon

  wicked-fast transcript quantification from RNA-seq data

• 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: 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

  Noutaa tiedostoja webistä

• rec: wham-align

  Wisconsin's High-Throughput Alignment Method

• sug: bcbio-doc

  Paketti ei saatavilla

• sug: cwltool

  Common Workflow Language reference implementation

• sug: kallisto

  near-optimal RNA-Seq quantification

• sug: libglu1-mesa

  Mesa OpenGL utility library (GLU)

• sug: qualimap

  Paketti ei saatavilla

• sug: r-other-wasabi

  prepare Sailfish and Salmon output for downstream analysis using GNU R

• sug: toil

  cross-platform workflow engine

• sug: tophat-recondition

  post-processor for TopHat unmapped reads

• sug: tophat2

  Paketti ei saatavilla

Imuroi bcbio

Imurointi kaikille saataville arkkitehtuureille

Arkkitehtuuri	Paketin koko	Koko asennettuna	Tiedostot
all	74.8 kt	280.0 kt	[tiedostoluettelo]