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Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Simple FASTQ quality assessment using Python
