Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: conda: bowtie2

View more package details: https://packages.ecosyste.ms/registries/anaconda.org/packages/bowtie2

Dependent Repos 147

miwipe/ngsLCA
  • environment.yaml

Size: 209 MB - Last synced: 9 months ago - Pushed: about 1 year ago

pcantalupo/pickaxe
Pickaxe is a viral discovery tool to help identify potential infectious agents in NGS sequencing reads
  • 2.3.3.* environment.yml

Size: 601 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago

vanheeringen-lab/genomepy
genes and genomes at your fingertips
  • environment.yml

Size: 11.1 MB - Last synced: about 24 hours ago - Pushed: 6 months ago

sternberglab/tnseq_pipeline
  • 2.4.5 environment.yml

Size: 243 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

cokelaer/rnaseq Fork of sequana/rnaseq
RNA-seq, QC and differential analysis pipeline
  • >=2.3 environment.yml

Size: 3.03 MB - Last synced: 2 months ago - Pushed: 3 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

onuryukselen/rnaseq
  • 2.3.5.* environment.yml

Size: 34.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

JetBrains-Research/snakecharm
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
  • 2.3.4.3 testData/wrappers_storage/bio/bismark/bismark/environment.yaml
  • 2.3.4.3 testData/wrappers_storage/bio/bismark/bismark2report/environment.yaml
  • 2.3.4.3 testData/wrappers_storage/bio/bismark/bismark_methylation_extractor/environment.yaml
  • 2.3.4.3 testData/wrappers_storage2/bio/bismark/custom_wr1/environment.yaml

Size: 2.93 MB - Last synced: 1 day ago - Pushed: 2 days ago

ccmbioinfo/crg2
Research pipeline for exploring clinically relevant genomic variants
  • 2.4.1 wrappers/fastq_screen/environment.yaml

Size: 4.48 MB - Last synced: 16 days ago - Pushed: 16 days ago

stajichlab/AAFTF
Automatic Assembly For The Fungi
  • environment.yml

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

TriLab-bioinf/HAASE_LAB_T12
Bulk RNAseq of nuclear export of RNAs AH6017 Pool3
  • 2.4.5.* environment.yml

Size: 17 MB - Last synced: about 1 year ago - Pushed: almost 2 years 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
  • 2.3.5 linux/sample/envs/environment.yml
  • 2.3.5.1 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
  • environment.yml

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

tdayris/snakemake-wrappers Fork of snakemake/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
  • 2.5.0.* bio/bismark/deduplicate_bismark/environment.yaml
  • 2.5.0.* bio/bowtie2/align/environment.yaml
  • 2.5.0.* bio/bowtie2/build/environment.yaml
  • 2.4.5.* bio/bismark/bam2nuc/environment.yaml
  • 2.5.0.* bio/bismark/bismark/environment.yaml
  • 2.4.5.* bio/bismark/bismark2bedGraph/environment.yaml
  • 2.5.0.* bio/bismark/bismark2report/environment.yaml
  • 2.4.5.* bio/bismark/bismark2summary/environment.yaml
  • 2.5.0.* bio/bismark/bismark_genome_preparation/environment.yaml
  • 2.5.0.* bio/bismark/bismark_methylation_extractor/environment.yaml
  • 2.5.0.* bio/fastq_screen/environment.yaml

Size: 735 MB - Last synced: 15 days ago - Pushed: 16 days ago

sateeshperi/reproduce_me
  • 2.3.5.1.* environment.yml

Size: 8.79 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

ribosomeprofiling/riboflow
Pipeline for Ribosome Profiling Data
  • 2.3.4.3.* environment.yaml

Size: 246 KB - Last synced: 2 months ago - Pushed: 11 months ago

kblin/covid-spike-classification
Detect interesting SARS-CoV-2 spike protein variants from Sanger sequencing data.
  • 2.4.2 environment.yml

Size: 144 KB - Last synced: 3 days ago - Pushed: about 2 years ago

GuilleGorines/nfcore-pikavirus-legacy 📦
  • 2.4.1.* environment.yml

Size: 348 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

khigashi1987/CUTRUN_Nextflow
CUT&RUN-seq analysis pipeline built using Nextflow.
  • 2.4.2.* docker/environment.yml

Size: 940 KB - Last synced: 9 months ago - Pushed: over 3 years ago

oalmelid/baal-nf-env
Docker environment for the non-R components of baal-nf
  • 2.3.* env/environment.yml

Size: 20.5 KB - Last synced: 7 months ago - Pushed: over 1 year ago

luisacusick/VC-Optimus
Bioinformatics pipeline to take short reads, align them to a reference, and call SNPs.
  • 2.3.5.1 environment.yml

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

lfnothias/qiime2
  • 2.4.2.* environment.yml

Size: 21.5 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

rchapman2000/de-novo-assembly-pipeline
  • 2.4.5 environment.yml

Size: 60.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

onuryukselen/chipseq
  • 2.3.5.* environment.yml

Size: 21.7 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

vihoikka/spacerAQ_vh
Custom code for analyzing data in Hoikkala et al. 2021 (DOI: https://doi.org/10.1128/mBio.03338-20)
  • 2.3.0.* environment.yml

Size: 8.46 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

Kange2014/ion-meta
A workflow using snakemake to analyze ion torrent based metagenomics data
  • envs/environment.yaml

Size: 16.7 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

aemann01/diet_calculus
Detection of diet from archaeological dental calculus project
  • 2.2.5.* 01-example_mapdamage/environment.yml
  • 2.4.2.* environment.yml

Size: 40.8 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

AndreaMariani-AM/Docker
This repo contains github actions to build various Docker Images
  • ChIPseq-snakemake/environment.yml
  • 2.3.5.* HiC-snakemake/environment.yml

Size: 322 KB - Last synced: 10 months ago - Pushed: 10 months ago

MPI-SHH-SummerSchool/dag-material
  • 2.4.4.* Hands on Introduction to Ancient Microbiome Analysis/environment.yml

Size: 489 MB - Last synced: 9 months ago - Pushed: over 2 years ago

evoosa/16S_bacteria_detector
Gets the frequency of bacterias for 16S RRNA sequences using the available algorithms
  • 2.4.1 src/environment.yml

Size: 97.4 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

SherineAwad/StructureVariations
Snakemake pipeline for detecting, annotating, filtering and visualising structure variations and gene fusions from WGS/WES.
  • 2.3.5.1.* environment.yml

Size: 548 KB - Last synced: 9 months ago - Pushed: over 1 year ago

isb-cgc/RunningWorkflows-on-the-GoogleCloud
  • 2.3.5.1.* Snakemake-GCgather/environment.yml
  • 2.3.5.1.* Snakemake-RNAseq/environment.yml

Size: 26.9 MB - Last synced: about 2 months ago - Pushed: about 2 years ago

bioinfo-pf-curie/ATAC-seq
Nextflow pipeline for ATAC-seq data analysis
  • 2.3.5.1 environment.yml

Size: 3.41 MB - Last synced: 5 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
  • 2.4.2 bio/bismark/bam2nuc/environment.yaml
  • 2.4.2 bio/bismark/bismark/environment.yaml
  • 2.4.2 bio/bismark/bismark2bedGraph/environment.yaml
  • 2.4.2 bio/bismark/bismark2report/environment.yaml
  • 2.4.2 bio/bismark/bismark2summary/environment.yaml
  • 2.4.2 bio/bismark/bismark_genome_preparation/environment.yaml
  • 2.4.2 bio/bismark/bismark_methylation_extractor/environment.yaml
  • 2.4.2 bio/bismark/deduplicate_bismark/environment.yaml
  • 2.4.* bio/bowtie2/align/environment.yaml
  • 2.4.* bio/bowtie2/build/environment.yaml
  • 2.2.6 bio/fastq_screen/environment.yaml

Size: 217 MB - Last synced: 1 day ago - Pushed: 1 day ago

tgstoecker/MuWU
Mu-seq Workflow Utility
  • 2.4.1 tests/MuWU_ITIS_test_with_mping_TE/workflow/builds/MuWU_bowtie2/bowtie2_align/environment.yaml
  • 2.4.1 tests/MuWU_ITIS_test_with_mping_TE/workflow/builds/MuWU_bowtie2/bowtie2_align_GENERIC/environment.yaml
  • 2.4.1 tests/MuWU_ITIS_test_with_mping_TE/workflow/builds/MuWU_bowtie2/bowtie2_build/environment.yaml
  • 2.4.1 tests/MuWU_test_germinal_Mutator/workflow/builds/MuWU_bowtie2/bowtie2_align/environment.yaml
  • 2.4.1 tests/MuWU_test_germinal_Mutator/workflow/builds/MuWU_bowtie2/bowtie2_align_GENERIC/environment.yaml
  • 2.4.1 tests/MuWU_test_germinal_Mutator/workflow/builds/MuWU_bowtie2/bowtie2_build/environment.yaml
  • 2.4.1 workflow/builds/MuWU_bowtie2/bowtie2_align/environment.yaml
  • 2.4.1 workflow/builds/MuWU_bowtie2/bowtie2_align_GENERIC/environment.yaml
  • 2.4.1 workflow/builds/MuWU_bowtie2/bowtie2_build/environment.yaml

Size: 69.2 MB - Last synced: 7 months ago - Pushed: 7 months ago

BorisYourich/EurOPDX-Galaxy
  • 2.3.4.1.* Docker image/pdx-analysis-workflows/JAX_RNA/rsem_alignment/environment.yml

Size: 2.27 MB - Last synced: 9 months ago - Pushed: 10 months ago

davidlevybooth/Rhodococcus_Transcriptomics
Rhodococcus Transcriptomic Pipeline
  • 2.3.4.3.* environment.yaml

Size: 21.5 KB - Last synced: about 1 year ago - Pushed: about 5 years ago

fmalmeida/MpGAP
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  • environment.yml

Size: 83.4 MB - Last synced: 3 months ago - Pushed: 3 months 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"
  • 2.3.4.1.* chip_seq/cidc_chips/environment.yml

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

Artur-man/slamseq_pipeline
  • 2.3.5.* environment.yml

Size: 456 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago

Ninomoriaty/m6APipe
  • 2.2.5 environment.yml

Last synced: about 1 year ago

Ninomoriaty/circPipe
FTW
  • 2.3.4.3.* environment.yml

Last synced: about 1 year ago

sgavril/Nugen-Pilot-Analysis
  • 2.4.2.* environment.yml

Size: 68.8 MB - Last synced: 10 months ago - Pushed: over 1 year ago

flatironinstitute/q2-matchmaker
A qiime2 plugin for case-control differential abundance analysis
  • 2.4.2 environment.yml

Size: 7.73 MB - Last synced: 9 months ago - Pushed: over 1 year 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.
  • 2.4.2.* environment.yml

Size: 10 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

maxibor/sam2lca_demo
sam2lca demo for JOBIM2022
  • environment.yml

Size: 10.5 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

canceromics/MeRIPseqPipe
MeRIPseqPipe：An integrated analysis pipeline for MeRIP-seq data based on Nextflow.
  • 2.2.5.* environment.yml

Size: 38 MB - Last synced: 10 days ago - Pushed: about 2 years ago

jlduan/fba
Tools for single-cell feature barcoding analysis
  • >=2.4.0 environment.yml

Size: 53.7 MB - Last synced: 1 day ago - Pushed: about 1 year ago

lcdb/lcdb-wf
Robust, tested workflows for RNA-seq, ChIP-seq and other high-throughput sequencing analysis
  • wrappers/wrappers/fastq_screen/environment.yaml

Size: 4.22 MB - Last synced: 1 day ago - Pushed: 1 day ago

snakemake/snakemake-wrappers
This repository contains wrapper scripts for fast integration of command line tools.
  • 2.3.5 bio/bowtie2/align/environment.yaml
  • 2.2.6 bio/fastq_screen/environment.yaml

Size: 13 MB - Last synced: over 1 year ago

liulab-dfci/CHIPS
A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data
  • 2.3.4.1.* environment.yml

Size: 65.1 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

aditi9783/ScarTrek
Python package for identifying genetic changes in whole-genome sequencing data
  • environment.yml

Size: 59.7 MB - Last synced: 4 days ago - Pushed: almost 3 years ago

adugduzhou/htgtsrep
  • environment.yml

Size: 165 MB - Last synced: over 1 year ago

antonisdim/haystac
Code repository for the HAYSTAC pipeline
  • 2.3.5.1.* haystac/environment.yaml

Size: 1.15 MB - Last synced: 2 months ago - Pushed: about 1 year ago

bokulich-lab/advanced-comp-bio-tutorial
Hands-on demonstration of 16S rRNA gene sequence analysis for SysBio Advanced Block Course 2022
  • 2.4.2 environment.yml

Size: 77.9 MB - Last synced: 12 months ago - Pushed: 12 months ago

BU-ISCIII/plasmidID
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
  • environment.yml

Size: 91.8 MB - Last synced: 7 months ago - Pushed: almost 3 years ago

ajodeh-juma/rvfv-amplicon-seq
A simple pipeline for Rift Valley fever virus consensus genome generation from amplicon sequencing
  • 2.4.2.* environment.yml

Size: 11.4 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

omicsclass/biodocker
docker images for bioinformatics
  • 2.4.1.* ampliseq-q2/environment.yml

Size: 59.2 MB - Last synced: 12 months ago - Pushed: over 1 year ago

durrantmm/mustache
A flexible tool to identify mobile genetic elements and their sites of insertions from short-read whole-genome sequencing data.
  • 2.3.4.3 envs/environment.yml

Size: 69.8 MB - Last synced: 12 days ago - Pushed: almost 5 years ago

FAANG/GSM-pipeline
  • 2.4.2.* environment.yml

Size: 18.8 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

lazyky/meripseqpipe
MeRIP-seq analysis pipeline arranged multiple alignment tools, peakCalling tools, Merge Peaks' methods and methylation analysis methods.
  • 2.2.5.* environment.yml

Size: 520 KB - Last synced: 7 months ago - Pushed: almost 3 years ago

bioinfo-pf-curie/annotationMaker
Build indexes and annotation files for Nextflow pipelines
  • 2.4.2 environment.yml

Size: 7.56 MB - Last synced: about 1 year ago - Pushed: over 1 year ago