seqassist

seqassist generates summary statistics and performs redundancy and nucleotide-level coverage analyses from NGS FASTQ data to support genome re-sequencing, RNA-Seq, and de novo genome sequencing and assembly experiments.

Key Features:

• Input Handling: Accepts NGS-generated FASTQ files as input.
• Alignment Methodology: Employs the BWA-MEM aligner for mapping reads to reference genomes.
• SA_RunStats Workflow: Reports counts of raw, cleaned, redundant, and unique reads, computes a redundancy rate, and lists unique sequences with their lengths and read counts.
• SA_Run2Ref Workflow: Estimates genome-wide coverage metrics including breadth, depth, and evenness at the nucleotide level.
• SA_Run2Run Workflow: Compares two NGS datasets to assess redundancy (overlapping rate) between runs.

Scientific Applications:

• Quality Evaluation: Provides coverage and redundancy statistics to assess the quality of DNA libraries for RNA-Seq or genome sequencing.
• Decision Support: Analyzes extent and uniformity of genomic locus coverage to inform the number of sequencing runs required for desired completeness.

Methodology:

Methodology is grounded in testing with synthetic datasets and real-world NGS datasets from genome re-sequencing experiments.