Bioinformatics Tools for Analyzing High Throughput Sequencing (NGS) Data

Commonly used tools in bioinformatics analyses of NGS dataset. Although, a lot of these tools can be used for other purposes too (such as microarray data, Sanger sequencing, proteomics).
This is a (non-exhaustive) list, but represents some of the most up-to-date and most commonly used tools.
Most of these tools are open source and free.
Most of these tools are manipulated from the command line, although some of them also provide a GUI (Graphical User Interface).

Next Generation Field Guide by Travis Glenn -Originally published in 2011 in Molecular Ecology Resources, but kept up to date every year. Thorough review of current sequencers, costs, pros and cons.

Picard Tools A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
FASTQC A quality control tool for high throughput sequence data.

The Genome Analysis Toolkit (GATK) -Software package developed at the Broad Institute to analyze high-throughput sequencing data.
bwa -Mapping sequences (e.g 454, Illumina) against a large reference genome, such as the human genome.
bowtie -Ultrafast, memory-efficient short read aligner.

trinity -Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
Trans-ABySS -de novo assembly of RNA-Seq data using ABySS
SOAPdenovo-Trans -de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts
MIRA -dSequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data.

soapdenovo2 Short-read assembly method that can build a de novo draft assembly for human-sized genomes.
https://www.ebi.ac.uk/~zerbino/velvet/Velvet -A sequence assembler for very short reads.
abyss -Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
MIRA -dSequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data.
IDBA-UD] for plastid reads, dealing quite well with uneven coverage * [[http://bioinf.spbau.ru/spades|SPADES for plastid reads, dealing quite well with uneven coverage

samtools -Samtools is a suite of programs for interacting with high-throughput sequencing data.
The Genome Analysis Toolkit (GATK) There are a variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

tassel -TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs.
stacks -Software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was 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.
pyRAD -pyRAD can analyze RAD, ddRAD, GBS, paired-end ddRAD and paired-end GBS data sets.

tophat -Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Usefull for analysing splice variants and their expression from NGS datasets
There are also several R packages listed here are specifically geared towards gene expression analyses

geneious -Comprehensive bioinformatics software platform.
CLC Genomics Workbench -CLC Genomics Workbench, for analyzing and visualizing next generation sequencing data.

Blast2GO -Functional annotation of (novel) sequences and the analysis of annotation data. Also has a GUI.
ErmineJ -Analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. Also has a GUI.
DAVID -Comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

See also this page on the wiki.
mothur -A comprehensive bioinformatics software platform for microbial ecology (eg. 16S rRNA gene sequences diversity)
Quantitative Insights Into Microbial Ecology (Qiime) -Another comprehensive bioinformatics software platform for microbial ecology primarily based on high-throughput amplicon sequencing data (such as SSU rRNA). Also has a GUI.