SERF

De Novo Sequence Analysis of Genomic Data from Next Generation Sequencers to identify biomarkers.

SERF MASK

De novo Identification and Masking of Repeats in Genomic Data from Next Generation Sequencers.

SERF DB

Database of results from SERF analysis of Genomes.

SERF CHART

Graphical data visualization of SERF analysis results

SERF UTILS

Cluster SERF analysis results by size, position, motif and totals

STAR

Alignment of large high-throughput sequencing reads to a reference genome.

BWA

Alignment of Short Reads from Next Generation Sequencers to a Reference Genome.

BOWTIE

Alignment of Short Reads from Next Generation Sequencers to a Reference Genome.

BOWTIE2

Alignment of Reads from Next Generation Sequencers to a Reference Genome.

SAMTOOLS

Manipulation of read alignments including sorting, merging, indexing, retrieval of reads and Mpileups.

BCFTOOLS

Analytics and utilities for CNVs, Consensus, Annotations and other Variant Calling using VCF or BCF data.

VCFTOOLS

Analytics and utilities for Variant Calling using VCF data.

CUTADAPT

Remove adapter sequences from high-throughput sequencing reads

CUFFLINKS

Transcript assembly, differential expression, and differential regulation for RNA-Seq

WGSIM

Generation of sequenced reads from a reference genome with SNPs and INDEL polymorphisms.