segemehl

segemehl maps short sequencing reads to reference genomes, detecting mismatches, insertions and deletions to support genomic, transcriptomic, and epigenomic analyses.

Key Features:

• Short-read mapping: Maps short sequencer reads to reference genomes.
• Mismatch and indel detection: Detects mismatches as well as insertions and deletions within reads.
• Flexible read-length support: Accurately maps reads of varying lengths, including reads contaminated with primer or polyadenylation sequences.
• Integration with "lack": Works with the "lack" tool to rescue unmapped RNA-seq reads and interoperates with split-read aligners.
• Applicability across data types: Supports analyses for genomic, transcriptomic, and epigenomic datasets.

Scientific Applications:

• Genomic investigations: Mapping reads to reference genomes for genomic studies across diverse species and tissues.
• Transcriptomic investigations: RNA-seq analyses, including rescuing unmapped reads in conjunction with "lack" and split-read aligners.
• Epigenomic investigations: Read alignment for epigenomic studies.

Methodology:

Performs short-read mapping with explicit detection of mismatches, insertions and deletions; supports variable read lengths and reads containing primer or polyadenylation sequences; integrates with "lack" and split-read aligners for rescuing unmapped RNA-seq reads.