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An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Accelerated BLAST compatible local sequence aligner.
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
C++ API & command-line toolkit for working with BAM data
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
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
SMC++ infers population history from whole-genome sequence data.
Scalable gVCF merging and joint variant calling for population sequencing projects
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
A pipeline used to identify different modes of duplicated gene pairs
A method for variant graph genotyping based on exact alignment of k-mers