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bcbio 的相关链接

Debian 的资源：

• 报告问题
• 开发者信息
• Debian Changelog
• 版权文件
• Debian 源代码仓库 (Git)
• Debian 补丁追踪网站

维护小组：

• Debian Med Packaging Team (QA 页面, 邮件存档)
• Steffen Moeller (QA 页面)

外部的资源：

• 主页 [github.com]

bcbio

toolkit for analysing high-throughput sequencing data

python3-bcbio

library for analysing high-throughput sequencing data

其他与 bcbio 有关的软件包

• adep: debhelper-compat (= 13)

  软件包暂时不可用

• adep: dh-sequence-python3

  本虚包由这些包填实： dh-python

• adep: python3-all

  package depending on all supported Python 3 runtime versions

• adep: python3-setuptools

  Python3 Distutils Enhancements

• adep: python3-gffutils

  Work with GFF and GTF files in a flexible database framework

• adep: python3-pandas

  data structures for "relational" or "labeled" data

• adep: python3-pybedtools

  Python 3 wrapper around BEDTools for bioinformatics work

• adep: python3-pysam

  interface for the SAM/BAM sequence alignment and mapping format (Python 3)

• adep: python3-toolz

  List processing tools and functional utilities

• adep: python3-tornado

  scalable, non-blocking web server and tools - Python 3 package

• adep: python3-yaml

  YAML parser and emitter for Python3

• adep: python3-scipy

  scientific tools for Python 3

• adep: python3-psutil

  module providing convenience functions for managing processes (Python3)

• adep: python3-joblib

  tools to provide lightweight pipelining in Python

• adep: atropos

  NGS read trimming tool that is specific, sensitive, and speedy

• adep: bcftools

  genomic variant calling and manipulation of VCF/BCF files

• adep: bedtools

  suite of utilities for comparing genomic features

• adep: biobambam2

  tools for early stage alignment file processing

• adep: bowtie2

  ultrafast memory-efficient short read aligner

• adep: bwa

  Burrows-Wheeler 比对工具

• adep: cnvkit

  Copy number variant detection from targeted DNA sequencing

• adep: fastqc

  quality control for high throughput sequence data

• adep: freebayes

  Bayesian haplotype-based polymorphism discovery and genotyping

• adep: gffread

  GFF/GTF format conversions, region filtering, FASTA sequence extraction

• adep: grabix

  wee tool for random access into BGZF files

• adep: gsort

  sort genomic data

• adep: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• adep: libfreetype6

  FreeType 2 字体引擎，共享库文件

• adep: lumpy-sv

  general probabilistic framework for structural variant discovery

• adep: mosdepth

  BAM/CRAM depth calculation biological sequencing

• adep: multiqc

  output integration for RNA sequencing across tools and samples

• adep: perl

  拉里 沃尔的实用报表提取语言(Perl)

• adep: libpicard-java

  Java library to manipulate SAM and BAM files

• adep: libvcflib-tools

  C++ library for parsing and manipulating VCF files (tools)

• adep: picard-tools

  Command line tools to manipulate SAM and BAM files

• adep: python3-biopython

  Python3 library for bioinformatics

• adep: python3-cyvcf2

  VCF parser based on htslib (Python 3)

• adep: python3-geneimpacts

  wraps command line tools to assess variants in gene sequences

• adep: python3-logbook

  logging system for Python that replaces the standard library's module (Python 3)

• adep: python3-requests

  elegant and simple HTTP library for Python3, built for human beings

• adep: python3-pytest

  Simple, powerful testing in Python3

• adep: python3-pytest-mock

  Thin wrapper around mock for easier use with pytest (Python 3 module)

• adep: pythonpy

  'python -c', with tab completion and shorthand

• adep: rapmap

  rapid sensitive and accurate DNA read mapping via quasi-mapping

• adep: rna-star

  ultrafast universal RNA-seq aligner

• adep: r-base-core

  GNU R core of statistical computation and graphics system

• adep: r-bioc-htsfilter

  GNU R filter replicated high-throughput transcriptome sequencing data

• adep: r-bioc-degreport

  BioConductor report of DEG analysis

• adep: r-bioc-purecn

  copy number calling and SNV classification using targeted short read sequencing

• adep: r-bioc-summarizedexperiment

  BioConductor assay container

• adep: r-cran-tidyverse

  Easily Install and Load the 'Tidyverse'

• adep: r-bioc-titancna

  Subclonal copy number and LOH prediction from whole genome sequencing

• adep: r-bioc-tximport

  transcript-level estimates for biological sequencing

• adep: r-other-wasabi

  prepare Sailfish and Salmon output for downstream analysis using GNU R

• adep: salmon

  wicked-fast transcript quantification from RNA-seq data

• adep: samblaster

  marks duplicates, extracts discordant/split reads

• adep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• adep: seqan-apps

  C++ library for the analysis of biological sequences

• adep: seqtk

  Fast and lightweight tool for processing sequences in the FASTA or FASTQ format

• adep: snpeff

  genetic variant annotation and effect prediction toolbox - tool

• adep: subread

  toolkit for processing next-gen sequencing data

• adep: tabix

  generic indexer for TAB-delimited genome position files

• adep: tophat-recondition

  post-processor for TopHat unmapped reads

• adep: umis

  tools for processing UMI RNA-tag data

• adep: vcfanno

  annotate a VCF with other VCFs/BEDs/tabixed files

• adep: vt

  toolset for short variant discovery in genetic sequence data

• adep: wham-align

  Wisconsin's High-Throughput Alignment Method

• adep: xonsh

  Python-powered, cross-platform, Unix-gazing shell

• adep: libhts-dev

  development files for the HTSlib

• adep: python3-sphinx

  documentation generator for Python projects

Download bcbio

Debian 软件包源码仓库（VCS：Git）

https://salsa.debian.org/med-team/bcbio.git

Debian 软件包源码仓库（可在线浏览）

https://salsa.debian.org/med-team/bcbio