Data

Tools

Indexes

Applications

Experiments

Open Source Science

denovo-rnaseq

De novo assembly, Differential gene expression, and annotation workflow

https://github.com/mr-eyes/denovo-rnaseq

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

De novo assembly, Differential gene expression, and annotation workflow

Basic Info
  • Host: GitHub
  • Owner: mr-eyes
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 1.79 MB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 0
  • Open Issues: 6
  • Releases: 2
Created about 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

denovo-rnaseq

DOI

Description

  • This is a simple Snakemake workflow to perform de novo transcriptome assembly, DGE, and annotation.
  • The workfow currently annotates the highly differential expressed genes with PVal of 0.005 and logfoldchange of 1.

Create conda enviornment

conda env create -f environment.yml conda activate rnaseq

Limitations

  • This workflow is meant to be easy to run, fast to implement, so it's currently not supporting flexibile configs.
  • If you need to change configuration and parameters you will need to edit the Snakefile.
  • It's only supporting RNASeq paired-end gzipped samples (not interleaved).

Main software used

  • Error trimming: fastp
  • De novo transcriptome assembly: rnaSpades
  • Quantification: Salmon
  • Differential gene expression: DESEQ2
  • Annotation: Trinotate

How to use?

  1. Create a working directory
  2. Change the ROOT_DIR in the Snakefile to match your working directory.
  3. Create a directory with the name samples inside the working directory.
  4. Put your samples in the samples directory with the naming convection:
    • R1: _1.fastq.gz
    • R2: _2.fastq.gz
  5. Copy paste the tab-delimited file samples.tsv in your workflow directory.
  6. Modify the samples.tsv to match your samples. Columns as following (sampletype, samplename, R1path, R2path).

You may use the following bash commands to update the Snakefile and samples.tsv files. bash curr=$(pwd)/workflow/ sed -i "s/REPLACE_ABSOLUTE_PATH/${curr//\//\\/}/g" workflow/samples.tsv sed -i "s/REPLACE_ROOT_DIR/${curr//\//\\/}/g" Snakefile

Workflow rulegraph

Owner

  • Name: Mohamed Abuelanin
  • Login: mr-eyes
  • Kind: user
  • Location: Davis, CA
  • Company: University of California, Davis

Computer Science Ph.D. Student

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Abuelanin
    given-names: Mohamed
    orcid: https://orcid.org/0000-0002-3419-4785
title: "De novo RNA-Seq Snakemake Workflow"
version: 1.0.1
date-released: 2023-01-05
url: "https://github.com/mr-eyes/denovo-rnaseq"

GitHub Events

Total
Last Year

Dependencies

environment.yml conda
  • _libgcc_mutex 0.1
  • _openmp_mutex 4.5
  • _r-mutex 1.0.1
  • _sysroot_linux-64_curr_repodata_hack 3
  • aioeasywebdav 2.4.0
  • aiohttp 3.7.4.post0
  • alsa-lib 1.1.5
  • amply 0.1.5
  • appdirs 1.4.4
  • async-timeout 3.0.1
  • atk-1.0 2.36.0
  • attmap 0.13.2
  • attrs 21.4.0
  • backports 1.0
  • backports.functools_lru_cache 1.6.4
  • bcrypt 3.2.0
  • binutils_impl_linux-64 2.36.1
  • binutils_linux-64 2.36
  • bioconductor-annotate 1.72.0
  • bioconductor-annotationdbi 1.56.1
  • bioconductor-biobase 2.54.0
  • bioconductor-biocfilecache 2.2.0
  • bioconductor-biocgenerics 0.40.0
  • bioconductor-biocio 1.4.0
  • bioconductor-biocparallel 1.28.3
  • bioconductor-biomart 2.50.0
  • bioconductor-biostrings 2.62.0
  • bioconductor-ctc 1.68.0
  • bioconductor-delayedarray 0.20.0
  • bioconductor-deseq2 1.34.0
  • bioconductor-dexseq 1.40.0
  • bioconductor-edger 3.36.0
  • bioconductor-genefilter 1.76.0
  • bioconductor-genelendatabase 1.30.0
  • bioconductor-geneplotter 1.72.0
  • bioconductor-genomeinfodb 1.30.0
  • bioconductor-genomeinfodbdata 1.2.7
  • bioconductor-genomicalignments 1.30.0
  • bioconductor-genomicfeatures 1.46.1
  • bioconductor-genomicranges 1.46.1
  • bioconductor-go.db 3.14.0
  • bioconductor-goseq 1.46.0
  • bioconductor-iranges 2.28.0
  • bioconductor-keggrest 1.34.0
  • bioconductor-limma 3.50.1
  • bioconductor-matrixgenerics 1.6.0
  • bioconductor-qvalue 2.26.0
  • bioconductor-rhtslib 1.26.0
  • bioconductor-rsamtools 2.10.0
  • bioconductor-rtracklayer 1.54.0
  • bioconductor-s4vectors 0.32.3
  • bioconductor-seqlogo 1.60.0
  • bioconductor-summarizedexperiment 1.24.0
  • bioconductor-xvector 0.34.0
  • bioconductor-zlibbioc 1.40.0
  • blast 2.12.0
  • boost-cpp 1.74.0
  • boto3 1.21.21
  • botocore 1.24.21
  • bowtie 1.0.0
  • bowtie2 2.3.4.3
  • brotlipy 0.7.0
  • bwidget 1.9.14
  • bzip2 1.0.8
  • c-ares 1.18.1
  • ca-certificates 2022.6.15
  • cachetools 5.0.0
  • cairo 1.16.0
  • certifi 2021.5.30
  • cffi 1.14.6
  • chardet 4.0.0
  • charset-normalizer 2.0.12
  • coin-or-cbc 2.10.8
  • coin-or-cgl 0.60.6
  • coin-or-clp 1.17.6
  • coin-or-osi 0.108.7
  • coin-or-utils 2.11.6
  • coincbc 2.10.8
  • configargparse 1.5.3
  • connection_pool 0.0.3
  • coreutils 8.25
  • cryptography 35.0.0
  • curl 7.83.1
  • datrie 0.8.2
  • decorator 4.4.2
  • defusedxml 0.7.1
  • docutils 0.17.1
  • dropbox 11.32.0
  • entrez-direct 16.2
  • expat 2.4.8
  • fastp 0.23.2
  • fftw 3.3.10
  • filechunkio 1.8
  • filelock 3.4.1
  • font-ttf-dejavu-sans-mono 2.37
  • font-ttf-inconsolata 3.000
  • font-ttf-source-code-pro 2.038
  • font-ttf-ubuntu 0.83
  • fontconfig 2.14.0
  • fonts-conda-ecosystem 1
  • fonts-conda-forge 1
  • freetype 2.10.4
  • fribidi 1.0.10
  • ftputil 5.0.4
  • gcc_impl_linux-64 10.3.0
  • gcc_linux-64 10.3.0
  • gdk-pixbuf 2.42.8
  • gettext 0.19.8.1
  • gfortran_impl_linux-64 10.3.0
  • gfortran_linux-64 10.3.0
  • ghostscript 9.54.0
  • giflib 5.2.1
  • gitdb 4.0.9
  • gitpython 3.1.18
  • gmp 6.2.1
  • google-api-core 2.8.0
  • google-api-python-client 2.51.0
  • google-auth 2.8.0
  • google-auth-httplib2 0.1.0
  • google-cloud-core 2.3.1
  • google-cloud-storage 2.4.0
  • google-crc32c 1.1.2
  • google-resumable-media 2.3.3
  • googleapis-common-protos 1.53.0
  • graphite2 1.3.13
  • graphviz 3.0.0
  • grpcio 1.38.1
  • gsl 2.7
  • gtk2 2.24.33
  • gts 0.7.6
  • gxx_impl_linux-64 10.3.0
  • gxx_linux-64 10.3.0
  • harfbuzz 4.2.0
  • hdf5 1.10.6
  • hmmer 3.3.2
  • htslib 1.14
  • httplib2 0.20.4
  • icu 69.1
  • idna 3.3
  • idna_ssl 1.1.0
  • imagemagick 7.1.0_29
  • importlib-metadata 4.8.1
  • importlib_metadata 4.8.1
  • iniconfig 1.1.1
  • ipython_genutils 0.2.0
  • isa-l 2.30.0
  • jbig 2.1
  • jinja2 3.0.3
  • jmespath 0.10.0
  • jpeg 9e
  • jsonschema 4.1.2
  • jupyter_core 4.8.1
  • kallisto 0.48.0
  • kernel-headers_linux-64 3.10.0
  • keyutils 1.6.1
  • kmer-jellyfish 2.3.0
  • krb5 1.19.3
  • lcms2 2.12
  • ld_impl_linux-64 2.36.1
  • lerc 3.0
  • libblas 3.9.0
  • libcblas 3.9.0
  • libcrc32c 1.1.2
  • libcurl 7.83.1
  • libdb 6.2.32
  • libdeflate 1.10
  • libedit 3.1.20191231
  • libev 4.33
  • libffi 3.4.2
  • libgcc 7.2.0
  • libgcc-devel_linux-64 10.3.0
  • libgcc-ng 12.1.0
  • libgd 2.3.3
  • libgfortran-ng 12.1.0
  • libgfortran5 12.1.0
  • libglib 2.70.2
  • libgomp 12.1.0
  • libiconv 1.16
  • libidn2 2.3.2
  • libjemalloc 5.2.1
  • liblapack 3.9.0
  • liblapacke 3.9.0
  • libnghttp2 1.47.0
  • libnsl 2.0.0
  • libopenblas 0.3.20
  • libpng 1.6.37
  • libprotobuf 3.18.0
  • librsvg 2.52.5
  • libsanitizer 10.3.0
  • libsodium 1.0.18
  • libssh2 1.10.0
  • libstdcxx-devel_linux-64 10.3.0
  • libstdcxx-ng 12.1.0
  • libtiff 4.4.0
  • libtool 2.4.6
  • libunistring 0.9.10
  • libuuid 2.32.1
  • libwebp 1.2.2
  • libwebp-base 1.2.2
  • libxcb 1.13
  • libxml2 2.9.12
  • libzlib 1.2.12
  • llvm-openmp 8.0.1
  • logmuse 0.2.6
  • lz4-c 1.9.3
  • make 4.3
  • markupsafe 2.0.1
  • more-itertools 8.13.0
  • multidict 5.2.0
  • nbformat 5.1.3
  • ncurses 6.3
  • networkx 2.5.1
  • numpy 1.19.5
  • oauth2client 4.1.3
  • openjdk 11.0.1
  • openjpeg 2.4.0
  • openmp 8.0.1
  • openssl 1.1.1o
  • packaging 21.3
  • pandas 1.1.5
  • pandoc 2.18
  • pango 1.50.7
  • paramiko 2.11.0
  • pcre 8.45
  • pcre2 10.37
  • peppy 0.31.2
  • perl 5.32.1
  • perl-app-cpanminus 1.7039
  • perl-archive-tar 2.40
  • perl-business-isbn 3.007
  • perl-business-isbn-data 20210112.006
  • perl-carp 1.38
  • perl-common-sense 3.75
  • perl-compress-raw-bzip2 2.103
  • perl-compress-raw-zlib 2.105
  • perl-constant 1.33
  • perl-cpan-meta 2.150010
  • perl-cpan-meta-requirements 2.140
  • perl-cpan-meta-yaml 0.018
  • perl-data-dumper 2.183
  • perl-db-file 1.855
  • perl-dbd-sqlite 1.70
  • perl-dbi 1.643
  • perl-encode 3.17
  • perl-exporter 5.72
  • perl-exporter-tiny 1.002002
  • perl-extutils-cbuilder 0.280230
  • perl-extutils-makemaker 6.66
  • perl-extutils-manifest 1.73
  • perl-extutils-parsexs 3.44
  • perl-file-find-rule 0.34
  • perl-file-path 2.09
  • perl-file-temp 0.2304
  • perl-getopt-long 2.52
  • perl-io-compress 2.106
  • perl-io-zlib 1.11
  • perl-ipc-cmd 1.04
  • perl-json 4.06
  • perl-json-pp 4.09
  • perl-json-xs 2.34
  • perl-list-moreutils 0.430
  • perl-list-moreutils-xs 0.430
  • perl-locale-maketext-simple 0.21
  • perl-mime-base64 3.16
  • perl-module-build 0.4231
  • perl-module-corelist 5.20220527
  • perl-module-load 0.34
  • perl-module-load-conditional 0.68
  • perl-module-metadata 1.000037
  • perl-number-compare 0.03
  • perl-params-check 0.38
  • perl-parent 0.236
  • perl-pathtools 3.75
  • perl-perl-ostype 1.010
  • perl-scalar-list-utils 1.62
  • perl-text-abbrev 1.02
  • perl-text-glob 0.11
  • perl-text-parsewords 3.31
  • perl-threaded 5.32.1
  • perl-types-serialiser 1.01
  • perl-uri 5.10
  • perl-version 0.9924
  • pip 21.3.1
  • pixman 0.40.0
  • pkg-config 0.29.2
  • pluggy 1.0.0
  • ply 3.11
  • prettytable 2.5.0
  • protobuf 3.18.0
  • psutil 5.8.0
  • pthread-stubs 0.4
  • pulp 2.5.1
  • py 1.11.0
  • pyasn1 0.4.8
  • pyasn1-modules 0.2.7
  • pycparser 2.21
  • pygments 2.12.0
  • pygraphviz 1.6
  • pynacl 1.4.0
  • pyopenssl 22.0.0
  • pyparsing 3.0.9
  • pyrsistent 0.17.3
  • pysftp 0.2.9
  • pysocks 1.7.1
  • pytest 6.2.5
  • python 3.6.15
  • python-dateutil 2.8.2
  • python-irodsclient 1.1.3
  • python_abi 3.6
  • pytz 2022.1
  • pyu2f 0.1.5
  • pyyaml 5.4.1
  • r-amap 0.8_18
  • r-ape 5.6_2
  • r-argparse 2.1.5
  • r-askpass 1.1
  • r-assertthat 0.2.1
  • r-backports 1.4.1
  • r-base 4.1.3
  • r-base64enc 0.1_3
  • r-bh 1.78.0_0
  • r-biasedurn 1.07
  • r-bit 4.0.4
  • r-bit64 4.0.5
  • r-bitops 1.0_7
  • r-blob 1.2.3
  • r-brio 1.1.3
  • r-broom 0.8.0
  • r-bslib 0.3.1
  • r-cachem 1.0.6
  • r-callr 3.7.0
  • r-catools 1.18.2
  • r-cellranger 1.1.0
  • r-cli 3.3.0
  • r-clipr 0.8.0
  • r-cluster 2.1.3
  • r-colorspace 2.0_3
  • r-cpp11 0.4.2
  • r-crayon 1.5.1
  • r-curl 4.3.2
  • r-data.table 1.14.2
  • r-dbi 1.1.2
  • r-dbplyr 2.2.0
  • r-desc 1.4.1
  • r-diffobj 0.3.5
  • r-digest 0.6.29
  • r-dplyr 1.0.9
  • r-dtplyr 1.2.1
  • r-ellipsis 0.3.2
  • r-evaluate 0.15
  • r-fansi 1.0.3
  • r-farver 2.1.0
  • r-fastcluster 1.2.3
  • r-fastmap 1.1.0
  • r-fastmatch 1.1_3
  • r-filelock 1.0.2
  • r-findpython 1.0.7
  • r-forcats 0.5.1
  • r-formatr 1.12
  • r-fs 1.5.2
  • r-futile.logger 1.4.3
  • r-futile.options 1.0.1
  • r-gargle 1.2.0
  • r-generics 0.1.2
  • r-ggplot2 3.3.6
  • r-glue 1.6.2
  • r-googledrive 2.0.0
  • r-googlesheets4 1.0.0
  • r-gplots 3.1.3
  • r-gtable 0.3.0
  • r-gtools 3.9.2.2
  • r-haven 2.5.0
  • r-highr 0.9
  • r-hms 1.1.1
  • r-htmltools 0.5.2
  • r-httr 1.4.3
  • r-hwriter 1.3.2.1
  • r-ids 1.0.1
  • r-igraph 1.3.0
  • r-isoband 0.2.5
  • r-jquerylib 0.1.4
  • r-jsonlite 1.8.0
  • r-kernsmooth 2.23_20
  • r-knitr 1.39
  • r-labeling 0.4.2
  • r-lambda.r 1.2.4
  • r-lattice 0.20_45
  • r-lifecycle 1.0.1
  • r-locfit 1.5_9.5
  • r-lubridate 1.8.0
  • r-magrittr 2.0.3
  • r-mass 7.3_57
  • r-matrix 1.4_1
  • r-matrixstats 0.62.0
  • r-memoise 2.0.1
  • r-mgcv 1.8_40
  • r-mime 0.12
  • r-modelr 0.1.8
  • r-munsell 0.5.0
  • r-nlme 3.1_158
  • r-openssl 2.0.2
  • r-phangorn 2.9.0
  • r-pillar 1.7.0
  • r-pkgconfig 2.0.3
  • r-pkgload 1.2.4
  • r-plogr 0.2.0
  • r-plyr 1.8.7
  • r-png 0.1_7
  • r-praise 1.0.0
  • r-prettyunits 1.1.1
  • r-processx 3.6.0
  • r-progress 1.2.2
  • r-ps 1.7.0
  • r-purrr 0.3.4
  • r-quadprog 1.5_8
  • r-r6 2.5.1
  • r-rappdirs 0.3.3
  • r-rcolorbrewer 1.1_3
  • r-rcpp 1.0.8.3
  • r-rcpparmadillo 0.11.2.0.0
  • r-rcurl 1.98_1.7
  • r-readr 2.1.2
  • r-readxl 1.4.0
  • r-rematch 1.0.1
  • r-rematch2 2.1.2
  • r-reprex 2.0.1
  • r-reshape2 1.4.4
  • r-restfulr 0.0.14
  • r-rjson 0.2.21
  • r-rlang 1.0.2
  • r-rmarkdown 2.14
  • r-rprojroot 2.0.3
  • r-rsqlite 2.2.8
  • r-rstudioapi 0.13
  • r-rvest 1.0.2
  • r-sass 0.4.1
  • r-scales 1.2.0
  • r-selectr 0.4_2
  • r-sm 2.2_5.7
  • r-snow 0.4_4
  • r-statmod 1.4.36
  • r-stringi 1.7.6
  • r-stringr 1.4.0
  • r-survival 3.3_1
  • r-sys 3.4
  • r-testthat 3.1.4
  • r-tibble 3.1.7
  • r-tidyr 1.2.0
  • r-tidyselect 1.1.2
  • r-tidyverse 1.3.1
  • r-tinytex 0.40
  • r-tzdb 0.3.0
  • r-utf8 1.2.2
  • r-uuid 1.1_0
  • r-vctrs 0.4.1
  • r-vioplot 0.3.7
  • r-viridislite 0.4.0
  • r-vroom 1.5.7
  • r-waldo 0.4.0
  • r-withr 2.5.0
  • r-xfun 0.31
  • r-xml 3.99_0.9
  • r-xml2 1.3.3
  • r-xtable 1.8_4
  • r-yaml 2.3.5
  • r-zoo 1.8_10
  • ratelimiter 1.2.0
  • readline 8.1.2
  • requests 2.28.0
  • rsa 4.8
  • s3transfer 0.5.2
  • salmon 1.8.0
  • samtools 1.15
  • sed 4.8
  • seqkit 2.2.0
  • setuptools 58.0.4
  • six 1.16.0
  • slacker 0.14.0
  • smart_open 6.0.0
  • smmap 3.0.5
  • snakemake 6.15.5
  • snakemake-minimal 6.15.5
  • spades 3.15.4
  • sqlite 3.38.5
  • stone 3.3.1
  • stopit 1.1.2
  • sysroot_linux-64 2.17
  • tabulate 0.8.9
  • tbb 2021.5.0
  • tk 8.6.12
  • tktable 2.10
  • toml 0.10.2
  • toposort 1.7
  • traitlets 4.3.3
  • transdecoder 5.5.0
  • trimmomatic 0.39
  • trinity 2.13.2
  • trinotate 3.2.2
  • typing-extensions 4.1.1
  • typing_extensions 4.1.1
  • ubiquerg 0.6.1
  • uritemplate 4.1.1
  • urllib3 1.26.9
  • veracitools 0.1.3
  • wcwidth 0.2.5
  • wget 1.20.3
  • wheel 0.37.1
  • wrapt 1.13.1
  • xorg-fixesproto 5.0
  • xorg-inputproto 2.3.2
  • xorg-kbproto 1.0.7
  • xorg-libice 1.0.10
  • xorg-libsm 1.2.3
  • xorg-libx11 1.7.2
  • xorg-libxau 1.0.9
  • xorg-libxdmcp 1.1.3
  • xorg-libxext 1.3.4
  • xorg-libxfixes 5.0.3
  • xorg-libxi 1.7.10
  • xorg-libxrender 0.9.10
  • xorg-libxt 1.2.1
  • xorg-libxtst 1.2.3
  • xorg-recordproto 1.14.2
  • xorg-renderproto 0.11.1
  • xorg-xextproto 7.3.0
  • xorg-xproto 7.0.31
  • xz 5.2.5
  • yaml 0.2.5
  • yarl 1.6.3
  • zipp 3.6.0
  • zlib 1.2.12
  • zstd 1.5.2
.github/workflows/test_workflow.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite