Ecosyste.ms: Repos

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

Package Usage: conda: trimmomatic

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

Dependent Repos 56

onuryukselen/rnaseq
  • 0.39.* environment.yml

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

SystemsGenetics/GEMmaker
A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
  • 0.39.* environment.yml

Size: 12.8 MB - Last synced: about 2 months ago - Pushed: 4 months 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
  • 0.39.* environment.yml

Size: 17 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

villegar/DoGE
Differential Gene Expression Analysis Pipeline
  • 0.39.* environment.yml

Size: 16 MB - Last synced: 10 months ago - Pushed: almost 3 years ago

OSU-BMBL/PGRP-Grape-Grafting
Adapting Perennial Crops for Climate Change: Graft Transmissible Effects of Rootstocks on Grapevine Shoots
  • 0.39 environment.yml

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

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

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

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

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

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

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

onuryukselen/chipseq
  • 0.39.* environment.yml

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

marisalim/testing-Rstudio-binder
  • binder/environment.yml

Size: 646 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago

cjfiscus/Kmer-it
  • 0.36.* workflow/envs/environment.yaml

Size: 42 MB - Last synced: 10 months 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)
  • 0.36.* environment.yml

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

sib-swiss/spring_school_bioinformatics_microbiology
  • 0.39.* containers/container_jupyter/project3/environment.yml

Size: 58.9 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago

TheJacksonLaboratory/splicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipeline
  • 0.39.* containers/splicing-pipelines-nf/environment.yml

Size: 32.6 MB - Last synced: 2 months ago - Pushed: 11 months ago

Wiselab2/NGPINT
  • 0.39 environment.yml

Size: 300 MB - Last synced: 7 months ago - Pushed: over 2 years ago

tgstoecker/MuWU
Mu-seq Workflow Utility
  • 0.36 tests/MuWU_ITIS_test_with_mping_TE/workflow/builds/MuWU_trimmomatic/environment.yaml
  • 0.36 tests/MuWU_ITIS_test_with_mping_TE/workflow/builds/MuWU_trimmomatic/generic_SE/environment.yaml
  • 0.36 tests/MuWU_ITIS_test_with_mping_TE/workflow/builds/trimmomatic/PE/environment.yaml
  • 0.36 tests/MuWU_ITIS_test_with_mping_TE/workflow/builds/trimmomatic/SE/environment.yaml
  • 0.36 tests/MuWU_test_germinal_Mutator/workflow/builds/MuWU_trimmomatic/environment.yaml
  • 0.36 tests/MuWU_test_germinal_Mutator/workflow/builds/MuWU_trimmomatic/generic_SE/environment.yaml
  • 0.36 tests/MuWU_test_germinal_Mutator/workflow/builds/trimmomatic/PE/environment.yaml
  • 0.36 tests/MuWU_test_germinal_Mutator/workflow/builds/trimmomatic/SE/environment.yaml
  • 0.36 workflow/builds/MuWU_trimmomatic/environment.yaml
  • 0.36 workflow/builds/MuWU_trimmomatic/generic_SE/environment.yaml
  • 0.36 workflow/builds/trimmomatic/PE/environment.yaml
  • 0.36 workflow/builds/trimmomatic/SE/environment.yaml

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

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

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

mitoNGS/MToolBox_snakemake
MToolBox pipeline written in snakemake to allow a better scalability
  • 0.38.* envs/environment.yaml

Size: 2.17 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

faircloth-lab/illumiprocessor
pre-process illumina reads
  • 0.39.* etc/environment.yml

Size: 161 KB - Last synced: 5 days ago - Pushed: over 1 year ago

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

Size: 456 KB - Last synced: about 1 year ago - Pushed: almost 2 years 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.
  • 0.39.* environment.yml

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

snakemake/snakemake-wrappers
This repository contains wrapper scripts for fast integration of command line tools.
  • 0.36 bio/trimmomatic/pe/environment.yaml
  • 0.36 bio/trimmomatic/se/environment.yaml

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

kyleaoconnell22/RNA_seq_binder
  • 0.36 environment.yaml

Size: 86.9 KB - Last synced: 6 months ago - Pushed: over 2 years 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

MozesBlom/nf-polish
A reproducible pipeline for polishing DNA reads, with a particular focus on sequence data from museum specimens
  • 0.39 environment.yml

Size: 12.7 KB - Last synced: 2 months ago - Pushed: 2 months ago

BCCDC-PHL/troika-nf
A Nextflow wrapper for the Troika pipeline
  • 0.39.* environments/environment.yml

Size: 9.77 KB - Last synced: about 1 month ago - Pushed: over 2 years ago

onuryukselen/trnaseq
  • 0.39.* environment.yml

Size: 770 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

onuryukselen/ribosome-profiling
  • 0.39.* environment.yml

Size: 4.07 MB - Last synced: 8 months ago - Pushed: 8 months ago

kirbyvisp/marmo
MARMO is a Modular and Robust pipeline for iMmune single-cell multi-Omics implemented in Snakemake.
  • 0.36 environment.yaml

Size: 2.86 MB - Last synced: over 1 year ago

kirbyvisp/vdjpuzzle
  • 0.36.* environment.yml

Size: 37.8 MB - Last synced: over 1 year ago

mr-eyes/denovo-rnaseq
De novo assembly, Differential gene expression, and annotation workflow
  • 0.39 environment.yml

Size: 1.79 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

scilifelab-lts/lts-workflows-sm-metagenomics
  • lts_workflows_sm_metagenomics/envs/environment.yaml

Size: 428 MB - Last synced: over 1 year ago

gwcbi/haphpipe
NGS viral assembly and population genetics
  • 0.38 environment.yml

Size: 2.35 MB - Last synced: 7 months ago - Pushed: about 3 years ago

nf-core/crisprvar 📦
[WIP] Evaluate outcomes from genome editing experiments
  • 0.39.* environment.yml

Size: 84.3 MB - Last synced: 5 months ago - Pushed: over 1 year ago

michaelbale/JLab-IPSeqFlow
J-Lab nextflow repo hub
  • environment.yml

Size: 103 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

crimBubble/ECCsplorer
The ECCsplorer is a bioinformatics pipeline for the automated detection of extrachromosomal circular DNA (eccDNA) from paired-end read data of amplified circular DNA.
  • environment.yml

Size: 15.9 MB - Last synced: 8 months ago - Pushed: 8 months ago

med-team/plasmidid
mapping-based, assembly-assisted plasmid identification tool
  • environment.yml

Last synced: over 1 year ago

scilifelab-lts/b_henriques-normark_1606
  • 0.38 bianca-env/environment.yml
  • 0.39 envs/environment.yaml

Size: 30.6 MB - Last synced: over 1 year ago

gonzalosm98/scRNA-SeqAnalysis
  • 0.39 environment.yml

Size: 62.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

scilifelab-lts/n_street_1801
This is the Bitbucket repository for the N_Street_1801 (Functional insights into the impacts of nitrogen fertilisation on forest belowground fungal metacommunities) project.
  • 0.38 environment.yml

Size: 12.3 MB - Last synced: over 1 year ago

dib-lab/elvers
(formerly eelpond) an automated RNA-Seq workflow system
  • 0.38.* elvers/rules/trimmomatic/environment.yml

Size: 106 MB - Last synced: 5 months ago - Pushed: over 3 years ago

kirbyvisp/vdjpuzzle2
VDJPuzzle version 2
  • 0.36 environment.yaml

Size: 29.7 MB - Last synced: over 1 year ago

cgps/ghru/pipelines/dsl2/pipelines/read_polishing
  • 0.38.* environment.yml

Last synced: over 1 year ago

treangenlab/variphyer
  • environment.yml

Last synced: about 1 year ago

eilslabs_workflows/modules
  • 0.39.* fastq/fastq/trimmomatic/environment.yaml

Last synced: over 1 year ago

cgps/ghru/pipelines/snp_phylogeny
  • 0.38.* environment.yml

Last synced: over 1 year ago

hc27oclock/My-dockerfiles
Listing docker files used in https://hub.docker.com/u/hc27oclock
  • 0.39.* mambaforge_r/environment.yml

Size: 240 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

fieldima/adequacy_of_PCMs Fork of phylo-lab-usc/fiels_workbench
This repository contains all the scripts for analyzing the adequacy of the most commonly used phylogenetic comparative models for gene expression datasets.
  • 0.39 Normalization_Reanalysis/environment.yml

Size: 350 MB - Last synced: 12 months ago - Pushed: over 1 year ago

healthyPlant/PhytoPipe
  • environment.yaml

Size: 114 MB - Last synced: 5 months ago - Pushed: 5 months ago

percyfal/snakemake-rules
Library of snakemake rules.
  • environment.yaml

Size: 3.85 MB - Last synced: about 1 year ago - Pushed: over 5 years ago

NCBI-Hackathons/ATACFlow
An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter
  • 0.36.* environment.yml

Size: 768 MB - Last synced: about 1 month ago - Pushed: over 5 years ago

neavemj/JEV_assembly_pipe
Snakemake pipeline to assemble JEV genomes from primer tiling data
  • 0.39.* environment.yaml

Size: 265 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago

neavemj/mappd
Metagenomic Analysis Pipeline for Pathogen Discovery
  • 0.39 environment.yaml

Size: 924 KB - Last synced: 8 months ago - Pushed: 8 months ago

IanSudbery/alvarez_et_al
Code and other scripts for Alvarez-Beneyas et al 2020
  • 0.39 environment.yml

Size: 41.2 MB - Last synced: 10 months ago - Pushed: over 2 years ago

mestill7/HiC-fast
HiC processing pipeline for fast alignment
  • 0.39 environment.yaml

Size: 32.2 MB - Last synced: 2 months ago - Pushed: about 2 years ago

qqep685d/qtlseq-demo-on-binder
  • environment.yml

Size: 48.3 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

wuaipinglab/sra2variant
The pipeline to replace our CLC workbench
  • environment.yml

Size: 161 KB - Last synced: 7 months ago - Pushed: about 2 years ago

bioinformatics-lab/scratch
  • 0.36 environment.yml

Size: 10.8 MB - Last synced: about 1 year ago - Pushed: about 6 years ago

bioinformatics-lab/BioDragon
  • 0.36 environment.yml

Size: 10.9 MB - Last synced: about 1 year ago - Pushed: over 6 years ago

TheJacksonLaboratory/covid19splicing
Betacoronavirus splicing analysis
  • 0.39.* Snakemake/environment.yaml

Size: 30.4 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

EthanHolleman/GLOE-loops
Exploration of human GLOE-seq data and looking for possible connections to Rloop formation
  • 0.39 environment.yml

Size: 2.9 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

kelly-sovacool/tiger_salamander_project 📦
SNP pipeline using Snakemake for the Weisrock Lab's Tiger Salamander project.
  • config/environment.yml

Size: 96.7 MB - Last synced: 25 days ago - Pushed: over 4 years ago

davidlevybooth/Praxis
  • 0.38.* envs/environment.yaml

Size: 137 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

nephantes/barcodeseq
  • 0.39.* environment.yml

Size: 1.89 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

nephantes/variantfitness
  • 0.39.* environment.yml

Size: 1.08 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

nephantes/dcrispr
  • 0.39.* environment.yml

Size: 1.43 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

yztxwd/rna-seq-standard-pipeline
standard RNA-seq analysis pipeline (cloned from snakemake example workflow)
  • 0.36 wrappers/trimmomatic/pe/environment.yaml
  • 0.36 wrappers/trimmomatic/se/environment.yaml

Size: 505 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

petedprice/supergenev2
  • nextflow/environment.yml

Size: 51.8 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

petedprice/supergene
  • nextflow/environment.yml

Size: 5.86 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

ctb/2019-snakemake-ucdavis
Intro to workflows for efficient automated data analysis, using snakemake.
  • binder/environment.yml

Size: 50.9 MB - Last synced: about 1 year ago - Pushed: about 5 years ago

transXpress/transXpress-nextflow
transXpress: a Nextflow pipeline for rapid de novo transcriptome assembly and annotation
  • 0.39 environment.yml

Size: 47 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

jhgille2/cs590_2023
Random files for CS590 Spring 2023
  • 0.39 e9/environment.yml

Size: 39.7 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

michaelbale/JLab-ATACFlow
JLab Nextflow ATACSeq Pipeline
  • environment.yml

Size: 25.6 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

dridk/exome
exome pipeline made with snakemake
  • 0.36 environment.yml

Size: 27.3 KB - Last synced: 25 days ago - Pushed: over 6 years ago

Cibiv/ipoolseq-pipeline
A pipeline for the analysis of iPool-Seq data
  • >=0.39 environment.yaml

Size: 9.71 MB - Last synced: 2 months ago - Pushed: over 2 years ago

tobbyxy/rnaseq-kallisto
  • environment.yml

Size: 16.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

kathiehuang/haplotype_calling_pipeline
  • 0.38.* config/environment.yaml

Size: 2.65 GB - Last synced: about 1 year ago - Pushed: about 1 year ago

davidfdr99/RNA-X
Nextflow Pipeline for bulk RNA-seq data using Kallisto
  • 0.39.* environment.yml

Size: 72.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

gmagannaDevelop/NGS
  • 0.39 environment.yml

Size: 9.77 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

geocarvalho/smake-studies
Repository with codes used to study snakemake
  • 2019-ucdavis/binder/environment.yml

Size: 63.9 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

AstrobioMike/Elinne-RNA-binder
  • environment.yml

Size: 8.79 KB - Last synced: about 1 year ago - Pushed: about 4 years ago

Miachol/vdjpuzzle2
  • 0.36 environment.yaml

Size: 28.8 MB - Last synced: about 1 year ago - Pushed: about 5 years ago

Vikash84/viclara
  • 0.38.* environment.yaml

Size: 289 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago

alarawms/sunbeam Fork of sunbeam-labs/sunbeam
A robust, extensible metagenomics pipeline
  • 0.39.* environment.yml

Size: 1.3 MB - Last synced: 5 days ago - Pushed: about 4 years ago

shaneknapp/datahub Fork of berkeley-dsep-infra/datahub
JupyterHubs for use by Berkeley enrolled students
  • 0.39.* deployments/biology/image/environment.yml

Size: 71.4 MB - Last synced: 4 days ago - Pushed: 4 days ago