rebeccagarner
Scientist-in-training exploring past and present lake microbiomes
@dawalshlab Berkeley, CA
rebeccagarner's Stars
soedinglab/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
BenLangmead/bowtie2
A fast and sensitive gapped read aligner
soedinglab/hh-suite
Remote protein homology detection suite.
tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
wwood/CoverM
Read coverage calculator for metagenomics
GregoryFaust/samblaster
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
wilkox/treemapify
🌳 Draw treemaps in ggplot2
bluenote-1577/skani
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
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.
cytoscape/cytoscape-automation
Collection of scripts that include programmatic io and control of Cytoscape
linxingchen/cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
wwood/galah
More scalable dereplication for metagenome assembled genomes
philarevalo/PopCOGenT
Microbial Populations as Clusters Of Gene Transfer
pfasante/phd_thesis
PhD Thesis template rebuilding Aaron Turon's thesis
Shamir-Lab/SCAPP
SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z
apcamargo/prodigal-gv
A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes
phasegenomics/hic_qc
A (very) simple script to QC Hi-C data.
burstein-lab/genomic-nlp
KasperSkytte/mmgenome2
Tools for extracting individual genomes from metagenomes
michaelkyu/MobMess
Xiaoyu2425/mEQO
dyxstat/MetaCC
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Bobay-Ochman/ConSpeciFix
A process to better define speciation
bcthomas/shrinksam
C++ program to shrink the SAM file after a read-mapping
eitanyaffe/hpipe
macman123/plasmid_network_analysis
A collection of scripts used in the following research paper: https://doi.org/10.1101/785212
gregmcc97/H-LARGe
Workflow for host-linkage to antimicrobial resistance genes using metagenomic 3C/Hi-C data
alexcritschristoph/filter_reads.py
Filters BAM files created by bowtie2 for better read mapping. Use for genomes from metagenomes.
gregmcc97/3C-HiC_analysis