{"id":42778451,"url":"https://github.com/ccbr/hervx","last_synced_at":"2026-01-29T22:14:52.032Z","repository":{"id":41846137,"uuid":"293851678","full_name":"CCBR/HERVx","owner":"CCBR","description":"Pipeline to characterize Human Endogenous Retrovirus (HERV) expression","archived":false,"fork":false,"pushed_at":"2024-01-23T21:37:17.000Z","size":6030,"stargazers_count":4,"open_issues_count":0,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-09-09T23:30:31.285Z","etag":null,"topics":["docker","herv","telescope","wdl-workflow"],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CCBR.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-09-08T15:29:06.000Z","updated_at":"2024-10-03T16:48:37.000Z","dependencies_parsed_at":"2025-09-09T21:35:22.064Z","dependency_job_id":"07e7574f-7e06-4e29-8dc5-69d1497d16d1","html_url":"https://github.com/CCBR/HERVx","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/CCBR/HERVx","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FHERVx","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FHERVx/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FHERVx/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FHERVx/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CCBR","download_url":"https://codeload.github.com/CCBR/HERVx/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FHERVx/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28887209,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-29T21:06:44.224Z","status":"ssl_error","status_checked_at":"2026-01-29T21:06:42.160Z","response_time":59,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["docker","herv","telescope","wdl-workflow"],"created_at":"2026-01-29T22:14:51.095Z","updated_at":"2026-01-29T22:14:52.025Z","avatar_url":"https://github.com/CCBR.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# HERVx\n\n[![Build](https://github.com/CCBR/HERVx/workflows/ci/badge.svg)](https://github.com/CCBR/HERVx/actions) [![GitHub issues](https://img.shields.io/github/issues/CCBR/HERVx)](https://github.com/CCBR/HERVx/issues)  [![GitHub license](https://img.shields.io/github/license/CCBR/HERVx)](https://github.com/CCBR/HERVx/blob/master/LICENSE)  \n\n### Table of Contents\n1. [Introduction](#1-Introduction)  \n2. [Build Resources](#2-Build-Resources)  \n    2.1 [Bowtie2 Indices](#21-Bowtie2-indices)  \n    2.2 [Image from Dockerfile](#22-Image-from-Dockerfile)   \n3. [Run HERVx pipeline](#3-Run-HERVx-pipeline)  \n    3.1 [Using Singularity](#31-Using-Singularity)  \n    3.2 [Using Docker](#32-Using-Docker)  \n    3.3 [Using WDL and Cromwell](#33-Using-WDL-and-Cromwell)\n4. [TLDR](#4-TLDR)\n5. [References](#5-References)\n\n\n\n### 1. Introduction  \n**H**uman **E**ndogenous **R**etro**v**irus e**x**pression pipeline, as known as `HERVx`, is a containerized pipeline to characterize retrotranscriptome. Quantifying HERV expression is difficult due to their repetitive nature and the high degree of sequence similarity shared among subfamilies— leading to an inherit level of uncertainty during fragment assignment.\n\nHERVx calculates Human Endogenous Retrovirus (HERV) expression in paired-end\nRNA-sequencing data. The pipeline runs cutadapt\u003csup\u003e1\u003c/sup\u003e to remove adapter sequences and to perform quality-trimming, bowtie2\u003csup\u003e2\u003c/sup\u003e to align reads against the Human reference genome (hg38), SAMtools\u003csup\u003e3\u003c/sup\u003e to convert from SAM to BAM format  and to sort reads by name, and Telescope\u003csup\u003e4\u003c/sup\u003e to characterize Human Endogenous Retrovirus (HERV) expression.\n\n[Telescope](https://github.com/mlbendall/telescope) is a computational method that provides accurate estimation of transposable element expression. It directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model.\n\nThe Dockerfile will build cutadapt, bowtie2, SAMtools \u0026 HTSlib, and Telescope from scratch along with a few other tools. Small reference files are located in `/opt2/refs/` in the container's filesystem.\n\n### 2. Build Resources\nReference files, resources, and indices are bundled within the container's filesystem.\n\nCurrently, the following files are located in `/opt2/refs/`:\n - trimmonatic_TruSeqv3_adapters.fa\n - HERV_rmsk.hg38.v2.genes.gtf\n - HERV_rmsk.hg38.v2.transcripts.gtf\n - L1Base.hg38.v1.transcripts.gtf\n - retro.hg38.v1.transcripts.gtf\n\n\nBowtie2 indices for `hg38` are bundled in the container's filesystem in `/opt2/bowtie2/`. Other indices can be provided by mounting the host filesystem to this PATH (overrides current hg38 indices).\n\n#### 2.1 Bowtie2 indices\n```bash\n# Get UCSC hg38 genome\nwget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz\nzcat hg38.fa.gz \u003e hg38.fa\n\n# Build the indices\nmodule load singularity\nSINGULARITY_CACHEDIR=$PWD singularity pull -F docker://nciccbr/ccbr_telescope\nsingularity exec -B $PWD:$PWD ccbr_telescope_latest.sif bowtie2-build hg38.fa hg38\n```\n\n#### 2.2 Image from Dockerfile\nIn the example below, change `skchronicles` with your DockerHub username.\n\n```bash\n# See listing of images on computer\ndocker image ls\n\n# Build\ndocker build --tag=ccbr_telescope:v0.0.1 .\n\n# Updating tag(s) before pushing to DockerHub\ndocker tag ccbr_telescope:v0.0.1 skchronicles/ccbr_telescope:v0.0.1\ndocker tag ccbr_telescope:v0.0.1 skchronicles/ccbr_telescope        # latest\ndocker tag ccbr_telescope:v0.0.1 nciccbr/ccbr_telescope:v0.0.1\ndocker tag ccbr_telescope:v0.0.1 nciccbr/ccbr_telescope             # latest\n\n# Check out new tag(s)\ndocker image ls\n\n# Peak around the container: verify things run correctly\ndocker run -ti ccbr_telescope:v0.0.1 /bin/bash\n\n# Push new tagged image to DockerHub\ndocker push skchronicles/ccbr_telescope:v0.0.1\ndocker push skchronicles/ccbr_telescope:latest\ndocker push nciccbr/ccbr_telescope:v0.0.1\ndocker push nciccbr/ccbr_telescope:latest\n```\n\n### 3. Run HERVx pipeline\n#### 3.1 Using Singularity\n```bash\nmodule load singularity\n# Pull from DockerHub\nSINGULARITY_CACHEDIR=$PWD singularity pull -F docker://nciccbr/ccbr_telescope\n# Display usage and help information\nsingularity exec -B $PWD:$PWD ccbr_telescope_latest.sif HERVx -h\n# Run HERVx pipeline\nsingularity exec -B $PWD:$PWD ccbr_telescope_latest.sif HERVx -r1 tests/small_S25_1.fastq -r2 tests/small_S25_2.fastq -o ERV_hg38\n```\n\n#### 3.2 Using Docker\n```bash\n# Assumes docker in $PATH\ndocker run -v $PWD:/data2 nciccbr/ccbr_telescope:latest HERVx -r1 tests/small_S25.R1.fastq.gz -r2 tests/small_S25.R2.fastq.gz -o ERV_hg38\n```\n\n#### 3.3 Using WDL and Cromwell\n```bash\n# hervx is configured to use different cromwell execution backends: local or slurm\n# view the help page for more information\n./hervx --help\n\n# @local: uses local singularity cromwell backend\n# The local EXECUTOR will run serially on compute\n# instance. This is useful for testing, debugging,\n# or when a users does not have access to a high\n# performance computing environment.\n./hervx local -r1 tests/small_S25.R1.fastq.gz -r2 tests/small_S25.R2.fastq.gz --outdir ERV_hg38\n\n# @slurm: uses slurm and singularity cromwell backend\n# The slurm EXECUTOR will submit jobs to the cluster.\n# It is recommended running hervx in this mode.\n./hervx slurm -r1 tests/small_S25.R1.fastq.gz -r2 tests/small_S25.R2.fastq.gz --outdir ERV_hg38\n```\n\n### 4. TLDR\n **Reference files** are located in `/opt2/` of the container filesystem.  \n**Dockerfile** to build this image is located in `/opt2/Dockerfile`\\.  \n**Pull** latest image from [DockerHub](https://hub.docker.com/repository/docker/nciccbr/ccbr_telescope)  \n**Usage**  \n\u0026emsp;`singularity exec docker://nciccbr/ccbr_telescope HERVx -h`  \n\u0026emsp;`docker run nciccbr/ccbr_telescope:latest HERVx -h`\n\n### 5. References  \n\u003csup\u003e**1.**\tMartin, M. (2011). \"Cutadapt removes adapter sequences from high-throughput sequencing reads.\" EMBnet 17(1): 10-12.\u003c/sup\u003e  \n\u003csup\u003e**2.** Langmead, B. and S. L. Salzberg (2012). \"Fast gapped-read alignment with Bowtie 2.\" Nat Methods 9(4): 357-359.\u003c/sup\u003e  \n\u003csup\u003e**3.** Li, H., et al. (2009). \"The Sequence Alignment/Map format and SAMtools.\" Bioinformatics 25(16): 2078-2079.\u003c/sup\u003e  \n\u003csup\u003e**4.** Bendall, M. L., et al. (2019). \"Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.\" PLOS Computational Biology 15(9): e1006453.\u003c/sup\u003e\n\n\n\u003chr\u003e\n\u003cp align=\"center\"\u003e\n\t\u003ca href=\"#HERVx\"\u003eBack to Top\u003c/a\u003e\n\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fccbr%2Fhervx","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fccbr%2Fhervx","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fccbr%2Fhervx/lists"}