maxgmarin

maxgmarin's Stars

• igvteam/igv-reports

  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

  Language:Python356147757

• jenniferlu717/KrakenTools

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

  Language:Python332118792

• rpetit3/fastq-dl

  Download FASTQ files from SRA or ENA repositories.

  Language:Python31042425

• rvaser/spoa

  SIMD partial order alignment tool/library

  Language:C++166165135

• jdblischak/smk-simple-slurm

  A simple Snakemake profile for Slurm without --cluster-config

  Language:Shell15362119

• robert-haas/gravis

  Interactive graph visualizations with Python and HTML/CSS/JS.

  Language:HTML1122129

• neherlab/pangraph

  A bioinformatic toolkit to align genome assemblies into pangenome graphs

  Language:C1017277

• lh3/minipileup

  Simple pileup-based variant caller

  Language:C884166

• moshi4/ANIclustermap

  A tool for drawing ANI clustermap between all-vs-all microbial genomes

  Language:Python753159

• salzberg-lab/Balrog

  Bacterial Annotation by Learned Representation of Genes

  Language:Jupyter Notebook548105

• KamilSJaron/oh-know

  k-mer learning materials

  Language:Jupyter Notebook48739

• evolbioinfo/pastml

  Ancestral character reconstruction and visualisation for rooted phylogenetic trees

  Language:Python328246

• mooreryan/iroki

  Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.

  Language:HTML3011061

• WHops/NAHRwhals

  R package and wrapper functions for identifying serial structural variations from genome assemblies

  Language:R27252

• aertslab/nextcloud_share_url_downloader

  Download files from and list content of NextCloud (password protected) share directly from the command line without needing a webbrowser.

  Language:Shell245311

• manzt/scipy-2024-anywidget

  Language:Jupyter Notebook24206

• kwongj/maskrc-svg

  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG

  Language:Python20296

• maxgmarin/panqc

  A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses

  Language:Python16210

• alemenze/bact-builder

  Bact-Builder: Microbial de novo genome assembly pipeline

  Language:Nextflow12102

• akikuno/cstag

  Python module to manipulate and visualize minimap2's cs tag

  Language:Python101120

• comprna/Junckey

  Collection of scripts for computing PSI of junction clusters

  Language:Python7413

• COMBINE-lab/lr_quant_benchmarks

  A replicable and modular benchmark for long-read RNA transcript quantification methods

  Language:Python6311

• karel-brinda/attotree

  Rapid estimation of phylogenetic trees using sketching

  Language:Python62220

• pieterjanvc/seq2mgs

  A pipeline for generating custom metagenomes from existing FASTQ files

  Language:R6130

• human-pangenomics/HPRC_metadata

  Language:Shell5240

• lukebharrison/MTBC0

  Mycobacterium tuberculosis complex - Most recent common ancestor (MTBC0)

  Language:Shell5100

• dw-data/air-pollution-megacities

  Data and methodology behind this analysis.

  4201

• mooreryan/midpoint-root

  Simple ETE script for midpoint rooting trees

  Language:Python320

• johandahlberg/gatk

  GATK Official Release Repository

  Language:Java2303

• maxgmarin/Mtb-ISEMapper

  An end-to-end Snakemake pipeline for analysis of IS6110 transposon insertions in the M. tuberculosis genome

  Language:Python2100