RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
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Mummer alignment tool
Reads simulator
RNAseq analysis notes from Ming Tang
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
