Pinned Repositories
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
adegenet
adegenet: a R package for the multivariate analysis of genetic markers
Adjutant
Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents
ads1-notebooks
Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing
cutadapt
cutadapt removes adapter sequences from sequencing reads
tarah28's Repositories
tarah28/adegenet
adegenet: a R package for the multivariate analysis of genetic markers
tarah28/aneuploidy_detection
Script uses simply alignment and a hard threshold for deviation in order to detect changes in coverage
tarah28/asap-1
A scalable bacterial genome assembly, annotation and analysis pipeline
tarah28/awesome-nextflow
A curated list of nextflow based pipelines
tarah28/benchmark_microbiome_transformations
Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"
tarah28/bioinfo_notebook
tarah28/CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
tarah28/clinker
Gene cluster comparison figure generator
tarah28/coinfinder
A tool for the identification of coincident (co-occurring and avoiding) genes in pangenomes.
tarah28/COVID_data_science_misc
Data science scripts on COVID related things
tarah28/ffq
A tool to find sequencing data and metadata from public databases.
tarah28/genomics-data-index
Indexes genomes using SNVs, MLST, or kmers for rapid querying, clustering, and visualization.
tarah28/InSilico_PCR
extract long read subsequences from a pair of primers
tarah28/introverse
Documentation for beginners entering R and the tidyverse
tarah28/islandpath
IslandPath standalone software
tarah28/LORCAN
LOng Read Consensus ANalysis (LORCAN)
tarah28/mashtree
Create a tree using Mash distances
tarah28/Metagenomics-Index-Correction
tarah28/metagenomics_crash_course
tarah28/MicrobiomeAnalystR
A companion R package for the MicrobiomeAnalyst web server
tarah28/nanostripper
Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
tarah28/ncov-watch
Tools for detecting mutations of interest in SARS-CoV-2 sequencing results
tarah28/phastaf
Identify phage regions in bacterial genomes for masking purposes
tarah28/platon
Identification and characterization of bacterial plasmid contigs from short-read draft assemblies.
tarah28/ROSS
ROSS - Random Operations on Sequences Suite
tarah28/snipit
snipit: summarise snps relative to your reference sequence
tarah28/snvphyl-tools
Tools/scripts for the SNVPhyl whole genome phylogenomics pipeline
tarah28/staramr
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
tarah28/variant_definitions
tarah28/VCF-kit
VCF-kit: Assorted utilities for the variant call format