JunpengShi

JunpengShi's Stars

• chanzuckerberg/shasta

  [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

  Language:C++27159

• vgteam/vg

  tools for working with genome variation graphs

  Language:C++1.1k194

• lh3/gfatools

  Tools for manipulating sequence graphs in the GFA and rGFA formats

  Language:C20820

• chhylp123/hifiasm

  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

  Language:C++52986

• arq5x/lumpy-sv

  lumpy: a general probabilistic framework for structural variant discovery

  Language:C314118

• oushujun/EDTA

  Extensive de-novo TE Annotator

  Language:Perl33673

• xiaochuanle/MECAT2

  Language:C6818

• PacificBiosciences/pbmm2

  A minimap2 frontend for PacBio native data formats

  Language:Perl17027

• malonge/RaGOO

  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

  Language:Python17028

• DecodeGenetics/SViper

  Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

  Language:C++41

• liangclab/HERA

  Language:Perl7621

• xiaochuanle/NECAT

  Nanopore data assembler

  Language:C13323

• OpenGene/fastp

  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  Language:C++1.9k332

• lbcb-sci/ra

  Assembler for raw de novo genome assembly of long uncorrected reads.

  Language:Python384

• MariaNattestad/Assemblytics

  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

  Language:JavaScript13528

• TransDecoder/TransDecoder

  TransDecoder source

  Language:Perl26858

• PASApipeline/PASApipeline

  PASA software

  Language:Perl17258

• hardingnj/xpclr

  Code to compute the XP-CLR statistic to infer natural selection

  Language:Python8728

• gmarcais/Jellyfish

  A fast multi-threaded k-mer counter

  Language:C++463136

• KorfLab/SNAP

  Gene prediction software

  Language:C6017

• genome/pindel

  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

  Language:C++16389

• Nextomics/NextDenovo

  Fast and accurate de novo assembler for long reads

  Language:C36053

• lh3/minimap2

  A versatile pairwise aligner for genomic and spliced nucleotide sequences

  Language:C1.8k407

• ruanjue/wtdbg2

  Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

  Language:C50492

• guoweilong/cgmaptools

  toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR

  Language:C6126

• xiaochuanle/MECAT

  MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

  Language:C++10726