Paketti: multiqc (1.18+dfsg-1)

[ Source: multiqc  ]

output integration for RNA sequencing across tools and samples

The sequencing of DNA or RNA with current high-throughput technologies involves an array of tools and these are applied over a range of samples. It is easy to loose oversight. And gathering the data and forwarding them in a readable manner to the individuals who took the samples is a challenge for a tool in itself. Well. Here it is. MultiQC aggregates the output of multiple tools into a single report.

Reports are generated by scanning given directories for recognised log files. These are parsed and a single HTML report is generated summarising the statistics for all logs found. MultiQC reports can describe multiple analysis steps and large numbers of samples within a single plot, and multiple analysis tools making it ideal for routine fast quality control.

Muut pakettiin multiqc liittyvät paketit

• dep: fonts-glyphicons-halflings

  icons made for smaller graphic

• dep: libjs-bootstrap

  HTML, CSS and JS framework

• dep: libjs-jquery

  JavaScript library for dynamic web applications

• dep: libjs-jquery-tablesorter

  jQuery flexible client-side table sorting plugin

• dep: libjs-jquery-ui

  JavaScript UI library for dynamic web applications

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-click

  Wrapper around optparse for command line utilities - Python 3.x

• dep: python3-coloredlogs

  colored terminal output for Python 3's logging module

• dep: python3-distutils

  distutils package for Python 3.x

• dep: python3-humanfriendly

  Python3 library to make user friendly text interfaces

• dep: python3-humanize

  Python Humanize library (Python 3)

• dep: python3-importlib-metadata

  library to access the metadata for a Python package - Python 3.x

• dep: python3-jinja2

  small but fast and easy to use stand-alone template engine

• dep: python3-lzstring

  LZ-based compression algorithm for Python (Python 3 version)

• dep: python3-markdown

  text-to-HTML conversion library/tool (Python 3 version)

• dep: python3-matplotlib

  Python based plotting system in a style similar to Matlab (Python 3)

• dep: python3-networkx

  tool to create, manipulate and study complex networks (Python3)

• dep: python3-numpy

  Fast array facility to the Python language (Python 3)

• dep: python3-packaging

  core utilities for python3 packages

• dep: python3-pyaml-env

  Python3 YAML configuration with environment variables parsing

• dep: python3-requests

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

• dep: python3-rich

  render rich text, tables, progress bars, syntax highlighting, markdown and more

• dep: python3-rich-click

  creating beautiful command line interfaces for Python3

• dep: python3-simplejson

  simple, fast, extensible JSON encoder/decoder for Python 3.x

• dep: python3-spectra

  Easy color scales and color conversion for Python (Python 3 version)

• dep: python3-yaml

  YAML parser and emitter for Python3

• rec: libjs-filesaver

  Client-side, HTML5 library for saving local files

• rec: node-clipboard

  Node.js module to copy to clipboard without flash

• rec: pandoc

  general markup converter

• rec: texlive-xetex

  TeX Live: XeTeX and packages

• enh: adapterremoval

  rapid adapter trimming, identification, and read merging of gene sequences

• enh: afterqc

  Paketti ei saatavilla

• enh: bamtools

  toolkit for manipulating BAM (genome alignment) files

• enh: bbmap

  BBTools genomic aligner and other tools for short sequences

• enh: bcftools

  genomic variant calling and manipulation of VCF/BCF files

• enh: bcl2fastq

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• enh: biobambam2

  tools for early stage alignment file processing

• enh: biobloomtools

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• enh: biscuit

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• enh: bismark

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• enh: bowtie

  Ultrafast memory-efficient short read aligner

• enh: bowtie2

  ultrafast memory-efficient short read aligner

• enh: busco

  benchmarking sets of universal single-copy orthologs

• enh: clipandmerge

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• enh: clusterflow

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• enh: conpair

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• enh: cutadapt

  Clean biological sequences from high-throughput sequencing reads

• enh: damageprofiler

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• enh: dedup

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• enh: deeptools

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• enh: disambiguate

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• enh: dragen

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• enh: fastp

  Ultra-fast all-in-one FASTQ preprocessor

• enh: fastq-screen

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• enh: fastqc

  quality control for high throughput sequence data

• enh: featurecounts

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• enh: fgbio

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• enh: flash

  Fast Length Adjustment of SHort reads

• enh: flexbar

  flexible barcode and adapter removal for sequencing platforms

• enh: gatk

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• enh: goleft-indexcov

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• enh: happy

  Parser generator for Haskell

• enh: hicexplorer

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• enh: hicpro

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• enh: hicup

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• enh: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• enh: homer

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• enh: htseq

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• enh: interop

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• enh: ivar

  functions broadly useful for viral amplicon-based sequencing

• enh: jellyfish

  count k-mers in DNA sequences

• enh: kaiju

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• enh: kallisto

  near-optimal RNA-Seq quantification

• enh: kat

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• enh: kraken

  assigning taxonomic labels to short DNA sequences

• enh: leehom

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• enh: longranger

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• enh: macs2

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• enh: malt

  sequence alignment and analysis tool to process sequencing data

• enh: methylqa

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• enh: minionqc

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• enh: mirtop

  annotate miRNAs with a standard mirna/isomir naming

• enh: mirtrace

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• enh: mosdepth

  BAM/CRAM depth calculation biological sequencing

• enh: mtnucratio

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• enh: multivcfanalyzer

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• enh: peddy

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• enh: phantompeakqualtools

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• enh: picard-tools

  Command line tools to manipulate SAM and BAM files

• enh: preseq

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• enh: prokka

  rapid annotation of prokaryotic genomes

• enh: pycoqc

  computes metrics and generates Interactive QC plots

• enh: qorts

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• enh: qualimap

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• enh: quast

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• enh: rna-seqc

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• enh: rna-star

  ultrafast universal RNA-seq aligner

• enh: rockhopper

  system for analyzing bacterial RNA-seq data

• enh: rsem

  RNA-Seq by Expectation-Maximization

• enh: rseqc

  Paketti ei saatavilla

• enh: salmon

  wicked-fast transcript quantification from RNA-seq data

• enh: samblaster

  marks duplicates, extracts discordant/split reads

• enh: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• enh: sargasso

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• enh: seqyclean

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• enh: sexdeterrmine

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• enh: sickle

  windowed adaptive trimming tool for FASTQ files using quality

• enh: skewer

  post-processing of high-throughput DNA sequence reads

• enh: slamdunk

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• enh: snpeff

  genetic variant annotation and effect prediction toolbox - tool

• enh: snpsplit

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• enh: somalier

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• enh: sortmerna

  tool for filtering, mapping and OTU-picking NGS reads

• enh: stacks

  pipeline for building loci from short-read DNA sequences

• enh: supernova

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• enh: theta2

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• enh: trimmomatic

  flexible read trimming tool for Illumina NGS data

• enh: varscan2

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• enh: vcftools

  Collection of tools to work with VCF files

• enh: verifybamid

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Imuroi multiqc

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Arkkitehtuuri	Paketin koko	Koko asennettuna	Tiedostot
all	695.9 kt	3,530.0 kt	[tiedostoluettelo]