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bioconda-recipes

Conda recipes for the bioconda channel.

covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

covid-19-signal

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

damage

Estimate nucleobase damage from sequencing substitution artifacts

djerba

Create cancer bioinformatics reports from metadata and workflow output

dtwa

framefix

Adjust a FastA DNA genome file's ORFs to correct frameshifts by best Diamond match

genomeid

A scheme for calculating a unique identifier for any human DNA sample with genome/exome data

gumshoe

Supplemental Statistical Tests and Utilities for Kallisto/Sleuth RNASeq Analysis

ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

maxwell

Fast signal-level matching for direct RNA nanopore sequencing

minno

Automatically stop a MinION sequencing experiment after a specific amount of data has been collected.

nanostripper

Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria

ncov

Nextstrain build for novel coronavirus (nCoV)

ncov-ingest

A pipeline that can fetch the latest nCoV data from GISAID, transform it, and put it on S3

ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

nextclade

Assign SARS-CoV-2 clades in the browser

nybbler

Targeted subsampling of SARS-CoV-2 genome sequence ensembles used in genomic epidemiology

opendba

GPU-accelerated Dynamic Time Warp (DTW) Barycenter Averaging

pokay

Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes

real

Reproduction number Estimation Accounting for Lead time

rnaspace

RNA Sequence Picking After Cutting Enzymatically

sars-cov-2-transcriptome

Supplemental code for "the architecture of SARS-CoV-2 transcriptome" paper

squigglekit

SquiggleKit: A toolkit for manipulating nanopore signal data

static-museum-audio-guide

A Jekyll static site generator theme for building lightweight audio tours for exhibitions or museums.

taiyaki

Training models for basecalling Oxford Nanopore reads

tamor

Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake

trimiss

Evaluate mismatch sensitivity of every 3-mer context in a genome to PCR primers