helennit

helennit's Stars

• 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

• EBI-Metagenomics/mettannotator

  Language:Python575

• sarahtanja/coral-DNA-RNA-lab-extractions

  This repo tracks the lab-work done to extract holobiont DNA and cnidarian host RNA from *Montipora capitata* rice corals using the Zymo Quick-DNA/RNA Miniprep Plus Kit

  1

• kjenike/panagram

  Language:Python603

• steineggerlab/SeekRank

  Rank homologous protein sequences based on a regressor trained on experimental measures

  Language:Jupyter Notebook6

• geronimp/enrichM

  Toolbox for comparative genomics of MAGs

  Language:Python8022

• raw-lab/MetaCerberus

  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

  Language:HTML507

• frubino/mgkit

  MGKit: Metagenomics Framework

  Language:Python153

• statdivlab/radEmu

  Language:R508

• conchoecia/odp

  oxford dot plots

  Language:Python13710

• Matteopaluh/KEMET

  KEGG Module Evaluation Tool

  Language:Python266

• trimstray/the-book-of-secret-knowledge

  A collection of inspiring lists, manuals, cheatsheets, blogs, hacks, one-liners, cli/web tools and more.

  150k9.6k

• papers-we-love/papers-we-love

  Papers from the computer science community to read and discuss.

  Language:Shell88.4k5.8k

• broadinstitute/StrainGE

  strain-level analysis tools

  Language:Python3310

• mgalardini/pyseer

  SEER, reimplemented in python 🐍🔮

  Language:Python11127

• zellerlab/GECCO

  GEne Cluster prediction with COnditional random fields.

  Language:Python607

• antismash/antismash

  antiSMASH

  Language:Python19065

• Merck/deepbgc

  BGC Detection and Classification Using Deep Learning

  Language:Jupyter Notebook12727

• kblin/ncbi-genome-download

  Scripts to download genomes from the NCBI FTP servers

  Language:Python956175

• lh3/bwa

  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

  Language:C1.5k557

• bactopia/bactopia

  A flexible pipeline for complete analysis of bacterial genomes

  Language:Nextflow41772

• oschwengers/bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  Language:Python45255

• micans/mcl

  MCL, the Markov Cluster algorithm, also known as Markov Clustering, is a method and program for clustering weighted or simple networks, a.k.a. graphs.

  Language:C9312

• RabbitBio/RabbitTClust

  RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

  Language:C++443

• apcamargo/genomad

  geNomad: Identification of mobile genetic elements

  Language:Python19319

• bacpop/ggCaller

  Bifrost graph gene caller.

  Language:C++886

• Kalan-Lab/lsaBGC

  lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

  Language:Python374

• gtonkinhill/panstripe

  post processing of bacterial pangenome gene presence/absence matrices

  Language:R526

• gtonkinhill/panaroo

  An updated pipeline for pangenome investigation

  Language:Python26934

• Kalan-Lab/zol

  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

  Language:Python504