A useful tool that indexes large .vcf files
TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions.
Consistent quality and adapter trimming for RRBS or standard FastQ files
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Trinity assembles transcript sequences from Illumina RNA-Seq data.
C++ library and its applications to generate and process accurate consensus sequences
USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
a tool kit for processing next-gen sequencing data
SIFT 4G takes a query sequence and uses multiple alignment information to predict tolerated and deleterious substitutions for every position of the query sequence.
Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.
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