Trevoranz

Trevoranz's Stars

• lh3/minimap2

  A versatile pairwise aligner for genomic and spliced nucleotide sequences

  Language:C1.8k851.1k408

• bbuchfink/diamond

  Accelerated BLAST compatible local sequence aligner.

  Language:C++1k38698182

• kblin/ncbi-genome-download

  Scripts to download genomes from the NCBI FTP servers

  Language:Python94635144175

• tseemann/prokka

  :zap: :aquarius: Rapid prokaryotic genome annotation

  Language:Perl83047648226

• mikolmogorov/Flye

  De novo assembler for single molecule sequencing reads using repeat graphs

  Language:C78129695168

• voutcn/megahit

  Ultra-fast and memory-efficient (meta-)genome assembler

  Language:C++59237334135

• rrwick/Unicycler

  hybrid assembly pipeline for bacterial genomes

  Language:C++56130328131

• oschwengers/bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  Language:Python4381323153

• bactopia/bactopia

  A flexible pipeline for complete analysis of bacterial genomes

  Language:Nextflow4071451069

• marbl/Mash

  Fast genome and metagenome distance estimation using MinHash

  Language:C++3893316591

• tseemann/abricate

  :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

  Language:Perl3662920091

• CDCgov/SARS-CoV-2_Sequencing

  A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

  Language:Perl345541583

• broadinstitute/pilon

  Pilon is an automated genome assembly improvement and variant detection tool

  Language:Scala3403017060

• stamatak/standard-RAxML

  Language:C3294854193

• ncbi/pgap

  NCBI Prokaryotic Genome Annotation Pipeline

  Language:Common Workflow Language3093031390

• ncbi/amr

  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

  Language:C++2672611637

• tseemann/mlst

  :id: Scan contig files against PubMLST typing schemes

  Language:Shell1952313245

• tseemann/nullarbor

  :floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

  Language:Perl1352029437

• rpetit3/dragonflye

  :dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

  Language:Perl11443510

• Mykrobe-tools/mykrobe

  Antibiotic resistance prediction in minutes

  Language:Python1061110527

• jodyphelan/TBProfiler

  Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

  Language:Python1041630143

• CSB5/lofreq

  LoFreq Star: Sensitive variant calling from sequencing data

  Language:C1001013230

• SionBayliss/PIRATE

  A toolbox for pangenome analysis and threshold evaluation.

  Language:Perl9098529

• CFSAN-Biostatistics/snp-pipeline

  SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.

  Language:Python57182530

• tseemann/samclip

  Filter SAM file for soft and hard clipped alignments

  Language:Perl4631710

• klebgenomics/Kaptive

  Language:Python43102721

• iqbal-lab-org/clockwork

  CRyPTIC data processing pipelines

  Language:HTML3186822

• jodyphelan/tbdb

  Standard database for the TBProfiler tool

  Language:Python2863018

• jizhang-nz/fast-GeP

  Fast genealogical relationship evaluation of bacterial isolates with WGS data.

  Language:Perl124162

• tseemann/legsta

  🍗⭐ In silico Legionella pneumophila Sequence Based Typing

  Language:Perl710163