[ buster ] [ bullseye ] [ bookworm ] [ sid ]

原始碼套件：bcbio（1.2.9-2） [contrib]

bcbio 的相關連結

Debian 的資源：

維護小組：

外部的資源：

主頁 [github.com]

本原始碼套件構建了以下這些二進位制包：

bcbio: toolkit for analysing high-throughput sequencing data
python3-bcbio: library for analysing high-throughput sequencing data

其他與 bcbio 有關的套件

構建架構特定包依賴

構建架構獨立包依賴

adep: debhelper-compat (= 13)

套件暫時不可用
adep: dh-python

Debian helper tools for packaging Python libraries and applications
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-mock

Mocking and Testing Library (Python3 version)
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-pyvcf

本虛擬套件由這些套件填實： python3-vcf
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 Aligner
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: hts-nim-tools

tools biological sequences: bam-filter, count-reads, vcf-check
adep: libfreetype6

FreeType 2 font engine, shared library files
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

Larry Wall's Practical Extraction and Report Language
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-nose

test discovery and running for Python3 unittest
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: python3-seqcluster

analysis of small RNA in NGS data
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

檔案	大小（單位：kB）	MD5 校驗碼
bcbio_1.2.9-2.dsc	3。6 kB	5b492d7159f7da391433d3c73b6b1a6a
bcbio_1.2.9.orig.tar.gz	17，147。3 kB	f905ba65f95528306afd35e77e3b7257
bcbio_1.2.9-2.debian.tar.xz	14。6 kB	49a11974b87ddfb9462f7ca466af0fad

Debian 套件原始碼倉庫（VCS：Git）: https://salsa.debian.org/med-team/bcbio.git
Debian 套件原始碼倉庫（可線上瀏覽）: https://salsa.debian.org/med-team/bcbio