musquita

musquita's Stars

• Hydro3639/NanoPhase

  Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)

  Language:Shell251

• AllTheBacteria/Phylign

  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on a laptop within a few hours.

  Language:Python122

• berthubert/AllTheBacteria

  Follow up to Grace Blackwell's 661k dataset, for 2023

  Language:Python1

• jackchen129/MAGenie

  MAGenie: A bioinformatic pipeline to reconstruct draft metagenome-assembled genomes (MAGs).

  2

• gtonkinhill/panaroo

  An updated pipeline for pangenome investigation

  Language:Python26934

• colostatemeg/meglab-kraken-custom-db

  Kraken custom database with genomic sequences seperated from plasmid sequences.

  Language:Python2

• MrOlm/drep

  Rapid comparison and dereplication of genomes

  Language:Python26337

• felixgrunberger/microbepore

  This is the repository for the manuscript “Expanding the transcriptomic toolbox in prokaryotes by Nanopore sequencing of RNA and cDNA molecules.” In this study, we applied and benchmarked all currently available RNA-seq kits from Oxford Nanopore technologies to analyse RNAs in the prokaryotic model organism Escherichia coli K-12.

  Language:R51

• moshi4/pyGenomeViz

  A genome visualization python package for comparative genomics

  Language:Python28023

• nekokoe/Plasmer

  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

  Language:Perl403

• barricklab/breseq

  breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.

  Language:C++14921

• sanger-pathogens/circlator

  A tool to circularize genome assemblies

  Language:Python23359

• yyoshiaki/ikra

  RNAseq pipeline centered on Salmon

  Language:Shell2720

• CCB-SB/plsdb

  PLSDB pipeline to collect bacterial plasmids from NCBI

  Language:Python364

• gbouras13/dnaapler

  Reorients assembled microbial sequences

  Language:Python983

• AntonS-bio/entropy

  Compare genes across samples and generate phylogenetic tree based on most diverse genes.

  1

• oschwengers/bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  Language:Python44455

• knights-lab/SHOGUN

  SHallow shOtGUN profiler

  Language:Python5419

• Lagator-Group/Plasmid-Assembly-TF-Annotation-Snakemake

  Language:Python2

• epi2me-labs/wf-metagenomics

  Metagenomic classification of long-read sequencing data

  Language:Nextflow5923

• epi2me-labs/wf-bacterial-genomes

  Small variant calling for haploid samples

  Language:Python268

• epi2me-labs/wf-clone-validation

  Language:Nextflow2418

• epi2me-labs/wf-alignment

  Language:Nextflow2320

• epi2me-labs/wf-basecalling

  Language:Nextflow3313

• fbreitwieser/krakenuniq

  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

  Language:C++22443

• nanoporetech/dorado

  Oxford Nanopore's Basecaller

  Language:C++52763

• asrivathsan/ONTbarcoder

  Language:Python273

• RaverJay/CholerAegon

  Pipeline for assembly and antimicrobial resistance gene detection

  Language:Python91

• simanjo/B.NanoAmP

  Bacterial Nanopore Assembly Pipeline

  Language:Python7

• richardmleggett/MARTi

  Metagenomic Analysis in Real Time

  Language:Java182