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An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Parallel t-SNE implementation with Python and Torch wrappers.
Accelerated BLAST compatible local sequence aligner.
Versatile open-source tool for microbiome analysis
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
A single molecule sequence assembler for genomes large and small.
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Transcript assembly and quantification for RNA-Seq
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
RAxML Next Generation: faster, easier-to-use and more flexible
Toolset for SV simulation, comparison and filtering
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…