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NGS

Filtering trimming and viewing

http://hannonlab.cshl.edu/fastx_toolkit/- FASTX-Toolkit - FASTQ/A short-reads pre-processing tools

http://samtools.sourceforge.net/SAMtools - provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

https://broadinstitute.github.io/picardPicard - a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

http://www.broadinstitute.org/igv/  - Integrative Genome Viewer (IGV) for NGS data

 

RNA-seq

https://code.google.com/archive/p/rna-star/STAR: ultrafast universal RNA-seq aligner

http://bowtie-bio.sourceforge.net/index.shtmlBowtie is an ultrafast, memory-efficient short read aligner (mapper)

http://cole-trapnell-lab.github.io/cufflinks/  - Cufflinks - Transcriptome assembly and differential expression analysis for RNA-Seq.

http://deweylab.github.io/RSEM/README.htmlRSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data

https://ccb.jhu.edu/software/tophat/index.shtmlTopHat is a fast splice junction mapper for RNA-Seq reads

 

RAD-Sequencing and variant analysis tools

https://software.broadinstitute.org/gatk/documentation/quickstart- GATK stands for GenomeAnalysisToolkit. It is a collection of command-line tools for analyzing high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF, with a focus on variant discovery

Incorporates tools like:

https://www.broadinstitute.org/cancer/cga/mutect-Mutect for identification of somatic point mutations in next generation sequencing data of cancer genomes.

https://software.broadinstitute.org/gatk/documentation/toolsdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php-HaplotypeCaller  capable of detecting SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region


AftrRAD

Assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. AftrRAD is able to accurately assemble loci, while accounting for indel variation among alleles.

AgroMarker Finder (AMF)

A GUI software for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. AMF integrates sophisticated tools with self-developed algorithms.

RADIS - Analysis of RAD-seq data for InterSpecific phylogeny 

Automates and standardizes the analyses of RAD-seq data for phylogenetic inference. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point.

PredRAD

Provides answers for the design of a study using RAD-seq i.e  i) what is the best restriction enzyme to use to obtain a desired number of RAD tags in the organism of interest.

PyRAD

A pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets. PyRAD uses a wrapper around an alignment-clustering algorithm, which allows for indel variation within and between samples.

RADtools

Tools for processing RAD Sequencing Illumina reads.

RADtyping

A user-defined perl procedure for performing de novo RAD genotyping in mapping populations.

Rainbow

Provides an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method.

RApiD

A method for de novo assembly of paired-end RAD-seq data in order to produce extended contigs flanking a restriction site.

Rtd

Reference-free ddRADseq analysis tools.

SimRAD

An R package that performs in silico restriciton enzyme digests and fragment size selection as implemented in most restriction stie associated DNA polymrophism and genotyping by sequencing methods.

simRRLs  

A program to simulate raw RADseq-like sequence data with options to modify tree, population, sequencing, and formatting parameters. Its main purpose is for testing assembly methods on raw data. The data are output in raw fastq format.

Stacks

Developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.