samtools | conda | Package Usage

ifremer-bioinformatics/samba

Standardized and Automated MetaBarcoding Analyses workflow (Mirror)

1.9.* containers/longreads-1.0/environment.yml

Size: 109 MB - Last synced: 11 months ago - Pushed: 11 months ago

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

1.9 environment.yml

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

onecodex/sars-cov-2

SARS-CoV-2 variant calling and consensus assembly pipeline

environment.yml

Size: 913 KB - Last synced: 26 days ago - Pushed: 8 months ago

iossifovlab/gpf

GPF: Genotypes and Phenotypes in Families

1.15.1.* environment.yml

Size: 75.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

brucemoran/tumour_only

Tumour-only DNA sequencing analysis

1.10 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.

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

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

miwipe/ngsLCA

environment.yaml

Size: 209 MB - Last synced: 8 months ago - Pushed: about 1 year ago

ikmb/virus-pipe

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

1.10.* environment.yml

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

oeg-upm/TPDL2022_FAIROs

1.10.* experiment1/research_object/environment.yml

Size: 85.9 KB - Last synced: 9 months ago - Pushed: almost 2 years ago

ZhenyanLuo/FindPlantNLRs

1.9 environment.yml

Size: 361 KB - Last synced: 3 months ago - Pushed: 3 months ago

cokelaer/rnaseq Fork of sequana/rnaseq

RNA-seq, QC and differential analysis pipeline

>1.7 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

1.15.* environment.yml

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

truwl/capanno

cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.

1.8 workflows/biowdl/RNA-seq/0.2.0/BamMetrics/environment.yml

Size: 19.5 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

csoneson/ARMOR

Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

1.11.* envs/environment.yaml

Size: 28.9 MB - Last synced: 5 days ago - Pushed: 2 months ago

epiBioCore/Snakemake-Nanopolish-Methylation

1.10.* environment.yaml

Size: 52.7 KB - Last synced: 12 months ago - Pushed: about 3 years ago

onuryukselen/rnaseq

1.3.* environment.yml

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

salzman-lab/ReadZS

The Read Z-score (ReadZS) is a metric that summarizes the transcriptional state of a gene in a single cell.

1.13.* environment.yml

Size: 1020 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

mhammell-laboratory/TEsmall

A pipeline for profiling TE-derived small RNAs

environment.yaml

Size: 98.6 KB - Last synced: 2 months ago - Pushed: 2 months ago

JetBrains-Research/snakecharm

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

1.9 testData/wrappers_storage/bio/bismark/bismark/environment.yaml
1.9 testData/wrappers_storage/bio/bismark/bismark2report/environment.yaml
1.9 testData/wrappers_storage/bio/bismark/bismark_methylation_extractor/environment.yaml
1.9 testData/wrappers_storage/bio/bwa/mem/environment.yaml
1.9 testData/wrappers_storage/bio/hisat2/index/environment.yaml
1.10 testData/wrappers_storage/bio/samtools/bam2fq/interleaved/environment.yaml
1.10 testData/wrappers_storage/bio/samtools/depth/environment.yaml
1.10 testData/wrappers_storage/bio/samtools/sort/environment.yaml
1.9 testData/wrappers_storage2/bio/bismark/custom_wr1/environment.yaml

Size: 2.82 MB - Last synced: about 10 hours ago - Pushed: about 12 hours ago

ccmbioinfo/crg2

Research pipeline for exploring clinically relevant genomic variants

1.9 wrappers/bcftools/call/environment.yaml
1.9 wrappers/bwa/mem/environment.yaml
1.9 wrappers/bwa/sampe/environment.yaml
1.9 wrappers/bwa/samse/environment.yaml
1.9 wrappers/samblaster/environment.yaml
1.10 wrappers/samtools/bam2fq/interleaved/environment.yaml
1.10 wrappers/samtools/bam2fq/separate/environment.yaml
1.10 wrappers/samtools/depth/environment.yaml
1.10 wrappers/samtools/faidx/environment.yaml
1.10 wrappers/samtools/fastq/environment.yaml
1.10 wrappers/samtools/fixmate/environment.yaml
1.10 wrappers/samtools/flagstat/environment.yaml
1.10 wrappers/samtools/idxstats/environment.yaml
1.10 wrappers/samtools/index/environment.yaml
1.10 wrappers/samtools/merge/environment.yaml
1.10 wrappers/samtools/mpileup/environment.yaml
1.10 wrappers/samtools/sort/environment.yaml
1.10 wrappers/samtools/stats/environment.yaml
1.10 wrappers/samtools/view/environment.yaml

Size: 4.48 MB - Last synced: 6 days ago - Pushed: 6 days ago

sk-sahu/Snakeflows

Collective Snakemake workflows for easy and reproducible NGS data analysis.

1.9.* envs/environment.yaml

Size: 305 KB - Last synced: 9 months ago - Pushed: 9 months ago

stajichlab/AAFTF

Automatic Assembly For The Fungi

environment.yml

Size: 2.37 MB - Last synced: 3 months ago - Pushed: 9 months ago

bahlolab/PLASTER

Nextflow pipeline for long amplicon typing of PacBio SMRT sequencing data

1.10.* inst/environment.yml

Size: 42.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

UCB-stat-159-s22/hw07-hw07-group12

hw07-hw07-group12 created by GitHub Classroom

1.3.1 environment.yml

Size: 81.6 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

afuentri/B-MyRepCLL

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

1.7 environment.yml

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

TriLab-bioinf/HAASE_LAB_T12

Bulk RNAseq of nuclear export of RNAs AH6017 Pool3

1.14.* environment.yml

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

1.9.* environment.yaml

Size: 9.81 MB - Last synced: 3 months ago - Pushed: 3 months ago

metashot/docker

Metashot docker images

dockerfiles/anvio/7-1/environment.yml

Size: 1.35 MB - Last synced: 12 months ago - Pushed: 12 months ago

casrssk/WGS-analysis-in-C_trachomatis

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

Size: 7.39 MB - Last synced: 4 months ago - Pushed: about 2 years ago

yasinkaymaz/endSnakeTools

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

1.9.* environment.yml

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

czbiohub-sf/sc2-illumina-pipeline 📦

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

1.9.* environment.yaml

Size: 11.9 MB - Last synced: 11 months 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.

1.12.* environments/environment.yml

Size: 15.2 MB - Last synced: 11 days ago - Pushed: 12 days ago

ImperialCollegeLondon/ReCoDE_rnaseq_pipeline

A parallelised pipeline for the analysis of RNA sequencing data. This repository is part of Imperial College London's ReCoDE project, which aims to support teaching and learning in research computing and data science.