Commercial tools
Strand NGS
offers many different tools including alignment, RNA-Seq, DNA-Seq, ChIP-Seq, Small RNA-Seq, Genome Browser, visualizations, Biological Interpretation, etc. Supports workflows “one can import the sample data in...
http://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
More at http://busco.ezlab.org/
ratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.
It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...
www.yandell-lab.org - MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats,...
Integrated solutions * CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...
github.com - Pilon is a software tool which can be used to:
Automatically improve draft assemblies
Find variation among strains, including large event detection
Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads...
drive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW.
UPARSE >OTU clustering for 16S and other marker genes....
broadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...
github.com - Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or...