bwa | conda | Package Usage | Ecosyste.ms: Repos

GCJMackenzie/sarek Fork of nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

0.7.17 environment.yml

Size: 16.4 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

brucemoran/tumour_only

Tumour-only DNA sequencing analysis

0.7.17 environment.yaml

Size: 58.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

jingwora/bioinformatics-tools

The collection of bioinformatics tools and sample codes.

0.7.* tools/Snakemake/snakemake-tutorial/environment.yaml

Size: 272 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

mgalardini/pyseer

SEER, reimplemented in python 🐍🔮

environment.yml

Size: 73.4 MB - Last synced: 7 months ago - Pushed: 7 months ago

ikmb/virus-pipe

Pipeline to map and variant call a Sars-CoV2 sample from amplicon sequencing. De-novo assembly is available as option.

0.7.17.* environment.yml

Size: 1.65 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

oeg-upm/TPDL2022_FAIROs

0.7.17.* experiment1/research_object/environment.yml

Size: 85.9 KB - Last synced: 10 months ago - Pushed: almost 2 years ago

vanheeringen-lab/genomepy

genes and genomes at your fingertips

environment.yml

Size: 11.1 MB - Last synced: 4 days ago - Pushed: 6 months ago

wishabc/nf-allelic-mapping Fork of vierstralab/nf-allelic-mapping

Fork of nextflow pipeline for calling SNVs with WASP

environment.yml

Size: 196 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

JetBrains-Research/snakecharm

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

0.7.17 testData/wrappers_storage/bio/bwa/mem/environment.yaml

Size: 2.93 MB - Last synced: 4 days ago - Pushed: 5 days ago

ccmbioinfo/crg2

Research pipeline for exploring clinically relevant genomic variants

0.7.17 wrappers/bwa/aln/environment.yaml
0.7.17 wrappers/bwa/index/environment.yaml
0.7.17 wrappers/bwa/mem/environment.yaml
0.7.17 wrappers/bwa/mem-samblaster/environment.yaml
0.7.17 wrappers/bwa/sampe/environment.yaml
0.7.17 wrappers/bwa/samse/environment.yaml

Size: 4.48 MB - Last synced: 19 days ago - Pushed: 19 days ago

stajichlab/AAFTF

Automatic Assembly For The Fungi

environment.yml

Size: 2.37 MB - Last synced: 3 months ago - Pushed: 10 months ago

afuentri/B-MyRepCLL

pipeline for a consensus-oriented analysis of B-cell clones

0.7.17 environment.yml

Size: 291 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

JakeLehle/peakpuller

End-to-end ChIP-seq data analysis pipeline

environment.yml

Size: 2.04 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

jeszyman/basecamp

0.7.* environment.yaml

Size: 9.81 MB - Last synced: 4 months ago - Pushed: 4 months ago

metashot/docker

Metashot docker images

dockerfiles/anvio/7-1/environment.yml

Size: 1.35 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

casrssk/WGS-analysis-in-C_trachomatis

0.7.17 linux/sample/envs/environment.yml
0.7.17 mac/samples/envs/environment.yml

Size: 7.39 MB - Last synced: 5 months ago - Pushed: about 2 years ago

yasinkaymaz/endSnakeTools

This repository will base the snakemake pipelines for the 3'-end sequencing data analysis

0.7.* environment.yml

Size: 40 KB - Last synced: about 1 year ago - Pushed: about 2 years ago

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.

0.7.17.* environments/environment.yml

Size: 15.3 MB - Last synced: 4 days ago - Pushed: 4 days ago

tdayris/snakemake-wrappers Fork of snakemake/snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

0.7.17.* bio/bwa/aln/environment.yaml
0.7.17.* bio/bwa/index/environment.yaml
0.7.17.* bio/bwa/mem/environment.yaml
0.7.17.* bio/bwa/mem-samblaster/environment.yaml
0.7.17.* bio/bwa/sampe/environment.yaml
0.7.17.* bio/bwa/samse/environment.yaml
0.7.17.* bio/bwa/samxe/environment.yaml
0.7.17.* bio/bwa-memx/index/environment.yaml
0.7.17.* bio/bwa-memx/mem/environment.yaml

Size: 735 MB - Last synced: 18 days ago - Pushed: 19 days ago

Clinical-Genomics-Lund/SomaticPanelPipeline

0.7.17.* container/environment.yml

Size: 5.29 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

hivlab/virome-wrappers

snakemake wrappers

fastq_screen/environment.yaml

Size: 30.5 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

anwarMZ/nf-upcoast-v

Nextflow based WGS workflow for Vp (Will be updated later)

0.7.17.* environments/environment.yml

Size: 56.6 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

ngs-docs/2021-GGG298

Winter 2021, GGG 298 - Tools for Data Intensive Research - UC Davis

binder/environment.yml

Size: 4.39 MB - Last synced: 2 months ago - Pushed: about 3 years ago

dridk/Sars-CoV-2-NGS-pipeline

A simple snakemake pipeline to call variant from NGS data of Sars-CoV-2 genome

environment.yml

Size: 77.1 KB - Last synced: 25 days ago - Pushed: over 2 years ago

OSU-BMBL/PGRP-Grape-Grafting

Adapting Perennial Crops for Climate Change: Graft Transmissible Effects of Rootstocks on Grapevine Shoots

0.7.17 environment.yml

Size: 2.22 MB - Last synced: 21 days ago - Pushed: over 3 years ago

aCLImatise/CliHelpParser

Reads the output from CLI help commands, and generates machine readable schemas (CWL etc)

0.7.17 environment.yml

Size: 1.16 MB - Last synced: 24 days ago - Pushed: over 3 years ago

fargenfo/linkseq

A GATK best-practices pipeline adapted to 10x Genomics linked-reads.

0.7.17.* environment.yml

Size: 20.1 MB - Last synced: 7 months ago - Pushed: over 2 years ago

rworkflow/Rsnakemake

0.7.* inst/snakemake-tutorial-data/environment.yaml

Size: 4.57 MB - Last synced: 17 days ago - Pushed: over 3 years ago

marchoeppner/metagenomic-profiling

0.7.17.* environment.yml

Size: 133 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

luisacusick/VC-Optimus

Bioinformatics pipeline to take short reads, align them to a reference, and call SNPs.

0.7.17 environment.yml

Size: 138 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

brimittleman/Comparative_APA

Project for comparative APA- Start fall 2019

code/environment.yaml

Size: 245 MB - Last synced: 7 months ago - Pushed: over 3 years ago

Clinical-Genomics-Lund/nextflow_myeloid

Nextflow pipeline for analysis of the twist myeloid panel

0.7.17.* container/environment.yml

Size: 4.95 MB - Last synced: 8 months ago - Pushed: about 3 years ago

cjfiscus/Kmer-it

0.7.17.* workflow/envs/environment.yaml

Size: 42 MB - Last synced: 10 months ago - Pushed: over 3 years ago

nicolettelee/docker_demo

Exercise in using docker to perform bwa alignments and report out mapped reads.

environment.yml

Size: 6.84 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

artic-network/fieldbioinformatics Fork of zibraproject/zika-pipeline

The ARTIC field bioinformatics pipeline

0.7.17.* environment.yml

Size: 3.97 MB - Last synced: 9 months ago - Pushed: 9 months ago

BCCDC-PHL/dehost-and-verify-illumina

Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken

0.7.17 environments/environment.yml

Size: 848 KB - Last synced: about 1 month ago - Pushed: over 3 years ago

nibscbioinformatics/viralevo

0.7.17.* environment.yml

Size: 308 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

Clinical-Genomics-Lund/nextflow_microwgs

0.7.17.* container/environment.yml

Size: 89.8 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

spellsystems/nf-germline-mapping

0.7.17.* containers/nf-germline-snv/environment.yml

Last synced: about 1 year ago

med-team/nf-core-artic

nf-core ARTIC field bioinformatics viral genome pipeline

0.7.17.* environment.yml

Last synced: over 1 year ago

fshepherd13/dirty-mouse-virome

Code and documentation for Fay et al., 2021

0.7.* environment.yaml

Size: 1.37 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

BioinfoNet/TeachingJupyterNotebooks

Training materials for the Open Science Workshop held in Nariobi

0.7.17 environment.yml

Size: 16 MB - Last synced: about 1 year ago - Pushed: over 5 years ago

jjacobson95/Genomics-In-Action-Resources

0.7.17.* Metagenomics_Snakemake_Pipeline/environment.yaml
0.7.* Metatranscriptomics_Snakemake_Pipeline/environment.yaml

Size: 1.79 MB - Last synced: 6 months ago - Pushed: over 2 years ago

BCCDC-PHL/mpxv-artic-nf

0.7.17 environments/environment.yml

Size: 49.2 MB - Last synced: about 1 month ago - Pushed: 11 months ago

AnimalGenomicsETH/bovine-graphs

Integrate multiple genome assemblies into a pangenome graph

envs/environment.yml

Size: 23.4 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

manuelconst/WES-Somatic-Variant-Calling

LTO WES Workflow

0.7.17.* environment.yaml

Size: 711 KB - Last synced: over 1 year ago - Pushed: almost 3 years ago

bioinfo-pf-curie/ATAC-seq

Nextflow pipeline for ATAC-seq data analysis

0.7.17 environment.yml

Size: 3.41 MB - Last synced: 6 months ago - Pushed: over 1 year ago

cibinsb/snakemake-wrappers Fork of snakemake/snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

0.7.17 bio/bwa/aln/environment.yaml
0.7.17 bio/bwa/index/environment.yaml
0.7.* bio/bwa/mem/environment.yaml
0.7.17 bio/bwa/mem-samblaster/environment.yaml
0.7.17 bio/bwa/sampe/environment.yaml
0.7.17 bio/bwa/samse/environment.yaml
0.7.17 bio/bwa/samxe/environment.yaml

Size: 217 MB - Last synced: 4 days ago - Pushed: 4 days ago

NBISweden/snakemake_best_practice

Small snakemake best practice workflow

0.7.17.* environment.yaml

Size: 651 KB - Last synced: 2 months ago - Pushed: over 2 years ago

ctokheim/Cop1_Cell_2021

Code for "In vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target"

0.7.15.* chip_seq/cidc_chips/environment.yml

Size: 81.3 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

Ninomoriaty/ExomePipe

0.7.17.* environment.yml

Last synced: about 1 year ago

Ninomoriaty/m6APipe

0.7.17 environment.yml

Last synced: about 1 year ago

Ninomoriaty/circPipe

FTW

0.7.17.* environment.yml

Last synced: about 1 year ago

c6435/snakemake-basics

0.7.17.* environment.yaml

Last synced: over 1 year ago

jfnavarro/hla_pipeline

DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions

environment.yml

Size: 1.55 MB - Last synced: 7 months ago - Pushed: almost 3 years ago

FrickTobias/BLR

environment.yml

Size: 1.84 MB - Last synced: 8 months ago - Pushed: 8 months ago

ajodeh-juma/viclara

viclara is a bioinformatics analysis pipeline for classification and reference guided assembly of segmented viruses from metagenomics reads obtained on Illumina platform.