We evaluated three analytical pipelines (‘HugeSeq’, ‘SIMPLEX’ and ‘TREAT’) and three workflow systems (‘Galaxy’, ‘LONI’ and ‘Taverna’).
‘HugeSeq’  is a fully integrated pipeline for NGS analysis from aligning reads to the identification and annotation of variants (SNPs and INDELs for whole-genome and whole-exome sequencing data as well as CNVs and SVs for whole-genome data only). It consists of three main parts: (i) preparing and aligning reads, (ii) combining and sorting reads for parallel processing of variant calling and (iii) variant calling and annotating. The pipeline accepts as an input reads in FASTA or FASTQ format and outputs identified variants in VCF format, and SVs and CNVs in GFF format. Identified variants are further processed with ANNOVAR to include additional annotations.