lpoorvin

lpoorvin's Stars

• UCSC-nanopore-cgl/MarginPolish

  MarginPolish: Graph based assembly polishing

  Language:C469

• ythuang0522/homopolish

  High-quality Nanopore-only genome polisher

  Language:Python6912

• HaploKit/metagenome-asm

  Enhancing long read based strain-aware metagenome assembly

  Language:Shell2

• smdabdoub/kraken-biom

  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

  Language:Python5017

• lh3/miniasm

  Ultrafast de novo assembly for long noisy reads (though having no consensus step)

  Language:TeX30970

• lbcb-sci/raven

  De novo genome assembler for long uncorrected reads

  Language:C++21221

• lh3/minimap2

  A versatile pairwise aligner for genomic and spliced nucleotide sequences

  Language:C1.9k424

• ProwlerForNanopore/ProwlerTrimmer

  Trimming tool for Oxford Nanopore sequence data

  Language:Python221

• jenniferlu717/KrakenTools

  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

  Language:Python32592

• DerrickWood/kraken2

  The second version of the Kraken taxonomic sequence classification system

  Language:C++744274

• rrwick/Trycycler

  A tool for generating consensus long-read assemblies for bacterial genomes

  Language:Python31328

• BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa

  Language:HTML71

• MariaNattestad/Ribbon

  A genome browser designed for complex structural variants and long reads.

  Language:JavaScript27530

• genotoul-bioinfo/dgenies

  Dotplot large Genomes in an Interactive, Efficient and Simple way

  Language:JavaScript10313

• BioinformaticsCSU/MultiNanopolish

  Accelaration of Nanopolish algorithm

  Language:C51

• pirovc/genome_updater

  Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

  Language:Shell14615

• pirovc/ganon

  ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

  Language:Python9413

• claczny/VizBin

  Repository of our application for human-augmented binning

  Language:Java2714

• DiltheyLab/MetaMaps

  Long-read metagenomic analysis

  Language:Perl10023

• musyk07/18S-ITS1-5.8S-SIS-Database

  Concatenated Silva-UNITE database using lowest common ancestor

  Language:Shell32

• IGBB/keanu

  A tool for viewing the contents of metagenomic samples

  Language:Python92

• jade-nhri/CCBGpipe

  A pipeline for completing circular bacterial genomes using a sampling strategy

  Language:Python84

• xlinxlin/ont-ncct

  Pipeline with GUI for nanopore-sequencing.

  Language:Java22

• rrwick/Assembly-Dereplicator

  A tool for removing redundant genomes from a set of assemblies

  Language:Python7010

• MaestSi/MetONTIIME

  A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework

  Language:Nextflow8816

• wurmlab/sequenceserver

  Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

  Language:JavaScript274114

• bhattlab/lathe

  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

  Language:Python6918

• chanzuckerberg/shasta

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

  Language:C++27258

• khyox/recentrifuge

  Recentrifuge: robust comparative analysis and contamination removal for metagenomics

  Language:Python877

• rrwick/Bandage

  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

  Language:C++59598