RNA-Seq pipeline

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RNA-Seq pipeline

Here we provide the tools to perform paired end or single read RNA-Seq analysis including raw data quality control, differential expression (DE) analysis and functional annotation. As input files you may use either zipped fastq-files (.fastq.gz) or mapped read data (.bam files). In case of paired end reads, corresponding fastq files should be named using .R1.fastq.gz and .R2.fastq.gz suffixes.

Pipeline Workflow

All analysis steps are illustrated in the pipeline flowchart . Specify the desired analysis details for your data in the essential.vars.groovy file (see below) and run the pipeline rnaseq.pipeline.groovy as described here . A markdown file DEreport.Rmd will be generated in the output reports folder after running the pipeline. Subsequently, the DEreport.Rmd file can be converted to a final html report using the knitr R-package.

The pipelines includes

  • quality control of rawdata with FastQC and MultiQC
  • Read mapping to the reference genome using STAR
  • generation of bigWig tracks for visualisation of alignment with deeptools
  • Characterization of insert size for paired-end libraries
  • Read quantification with featureCounts (Subread)
  • Library complexity assessment with dupRadar
  • RNA class representation
  • Check for strand specificity
  • Visualization of gene body coverage
  • Illustration of sample relatedness with MDS plots and heatmaps
  • Differential Expression Analysis for depicted group comparisons with DESeq2
  • Enrichment analysis for DE results with clusterProfiler and ReactomePA
  • Additional DE analysis including multimapped reads

Code Snippets

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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    BASEOUTPUT=`basename $output` &&
    CHRSIZES=\${TMP}/\$(basename ${input.prefix}).bam2bw.chrsizes &&
    samtools idxstats ${input} | cut -f1-2 > \${CHRSIZES} &&
    TOTAL_MAPPED=\$( samtools flagstat $input | head -n5 | tail -n1 | cut -f1 -d" ") &&
    SCALE=\$(echo "1000000/\$TOTAL_MAPPED" | bc -l) &&
    genomeCoverageBed -bg -split -scale \${SCALE} -ibam ${input} | sortBed -i -  > \${TMP}/\${BASEOUTPUT%.bw}.bedgraph &&
    bedGraphToBigWig \${TMP}/\${BASEOUTPUT%.bw}.bedgraph \${CHRSIZES} \${TMP}/\${BASEOUTPUT} &&
    cp -f \${TMP}/\${BASEOUTPUT} $output
""","bam2bw"
Bpipe SAMtools bedGraphToBigWig From line 16 of NGS/bam2bw.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    bamCoverage $BAMCOVERAGE_FLAGS --bam $input -o ${output};
""","bamCoverage"
Bpipe DeepTools From line 20 of NGS/bamcoverage.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    samtools index $input
""","BAMindexer"
Bpipe SAMtools From line 15 of NGS/bamindexer.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    cutadapt $CUTADAPT_FLAGS $CUTADAPT_FLAGS_PAIRED $CUTADAPT_FLAGS_TOOLONG --too-short-output=\${TMP}/${SAMPLENAME_BASE}.cutadapt_discarded.fastq.gz --output=\${TMP}/${SAMPLENAME_BASE}.cutadapt.fastq.gz $input1 $CUTADAPT_INPUT_SECOND 1> ${CUTADAPT_STATSDIR}/${SAMPLENAME_BASE_PRUNED}.cutadapt.log &&

    mv -t ${CUTADAPT_DISCARDED_DIR}/ \${TMP}/${SAMPLENAME_BASE_PRUNED}*cutadapt_discarded*.fastq.gz &&
    mv -t $output.dir \${TMP}/${SAMPLENAME_BASE_PRUNED}*cutadapt.fastq.gz
""","Cutadapt"
Bpipe Cutadapt From line 50 of NGS/cutadapt.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    fastqc --extract $FASTQC_FLAGS -o $output.dir $inputs
""","FastQC"
Bpipe FastQC From line 18 of NGS/fastqc.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    if [ ! -e "$output.prefix" ]; then
        mkdir $output.prefix;
    fi &&
    fastqreference=${FastqScreen_vars.conf};
    references=(\${fastqreference//,/ });
    for i in "\${!references[@]}"; do
        reference=(\${references[i]//::/ });
        echo -e "DATABASE\t\${reference[0]}\t\${reference[1]}" >> $output.prefix/fastqscreen.conf;
    done;
    fastq_screen $FASTQSCREEN_FLAGS --conf $output.prefix/fastqscreen.conf --outdir $output.prefix $inputs;
    touch $outputs
""","FastqScreen"
Bpipe From line 18 of NGS/fastqscreen.groovy 
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exec """
     ${TOOL_ENV} &&
     ${PREAMBLE} &&

    chroms=\$(cut -f1 ${FilterChr_vars.file}) && 
    samtools view -@ ${FilterChr_vars.threads} -b $input \$chroms > $output &&
    samtools index $output
""","FilterChr"
Bpipe SAMtools From line 14 of NGS/filterchromosomes.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    java ${InsertSize_vars.java_flags} -jar \${PICARD} CollectInsertSizeMetrics $INSERTSIZE_FLAGS INPUT=$input OUTPUT=$output HISTOGRAM_FILE=${output.prefix}_hist.pdf
""","InsertSize"
Bpipe From line 20 of NGS/insertsize.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    bam dedup --in $input --out $output --log ${input.prefix}_dupmetrics.log --noPhoneHome
""","MarkDups2"
Bpipe From line 14 of NGS/markdups2.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    multiqc $ESSENTIAL_PROJECT $MultiQC_FLAGS -o $output.dir
""","MULTIQC"
Bpipe MultiQC From line 16 of NGS/multiqc.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    Rscript ${PIPELINE_ROOT}/tools/trackhub/Configure_Trackhub.R $TRACKHUB_FLAGS
""","trackhub_config"
Bpipe From line 26 of NGS/trackhub_config.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    Rscript ${PIPELINE_ROOT}/tools/trackhub/Make_Trackhub.R $TRACKHUB_FLAGS
""","trackhub"
Bpipe From line 17 of NGS/trackhub.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&
    echo $inputs > /dev/null &&

    Rscript ${PIPELINE_ROOT}/tools/DE_DESeq2/DE_DESeq2.R $DE_DESeq2_FLAGS
""","DE_DESeq2"
Bpipe From line 34 of RNAseq/deseq2.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&
    echo $inputs > /dev/null  &&

    if [[ ! -e "$INPUT_READS_DIR" ]]; then
        mkdir "$INPUT_READS_DIR";
    fi &&

    for f in $DE_DESeq2_MM_vars.dupradar_outdir/*.tsv; do
        F=\$(basename \$f) ;
        tail -n +2 $f | cut -f1,3 | sort -k1,1 > "$INPUT_READS_DIR/\${F%_dupRadar.tsv}.readcounts.tsv" ;
    done &&

    Rscript ${PIPELINE_ROOT}/tools/DE_DESeq2/DE_DESeq2.R $DE_DESeq2_MM_FLAGS
""","DE_DESeq2_MM"
Bpipe From line 36 of RNAseq/deseq2_mm.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    base=`basename $input` &&
    bamdupmark=\${TMP}/\${base%.bam}.dupmarked.bam &&

    bam dedup --in $input --out \${bamdupmark} --log ${output.dir}/\${base%.bam}_dupmetrics.log --noPhoneHome &&
    samtools index \${bamdupmark} &&

    if [[ "${dupRadar_vars.paired}" == "yes" ]]; then
        echo "We are resorting and doing the repair\n" &&
        bamrepair=\${TMP}/\${base%.bam}.dupmarked.repair.bam &&
        repair -i \${bamdupmark} -T ${dupRadar_vars.threads} -o \${bamrepair} &&
        Rscript ${PIPELINE_ROOT}/tools/dupRadar/dupRadar.R bam=\${bamrepair} $DUPRADAR_FLAGS;
    else
        Rscript ${PIPELINE_ROOT}/tools/dupRadar/dupRadar.R bam=\${bamdupmark} $DUPRADAR_FLAGS;
    fi
""","dupRadar"
Bpipe SAMtools From line 25 of RNAseq/dupradar.groovy 
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exec """
    ${PREAMBLE} &&

    tail -n +3 $input | awk '{print \$1\"\\t\"\$7}' > $output
"""
Bpipe From line 13 of RNAseq/filter2htseq.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    if [[ ! -e "$output.dir" ]]; then
        mkdir -p "$output.dir";
    fi &&

    Rscript ${PIPELINE_ROOT}/tools/geneBodyCov/geneBodyCov.R bam=$input $GENEBODYCOV2_FLAGS
""","geneBodyCov2"
Bpipe From line 22 of RNAseq/genebodycov2.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    touch $output &&
    Rscript ${PIPELINE_ROOT}/tools/GO_Enrichment/GO_Enrichment.R rData=$input $GO_Enrichment_FLAGS &&
    if [ \$? -ne 0 ]; then rm $output; fi;
""","GO_Enrichment"
Bpipe From line 24 of RNAseq/GO_Enrichment.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    infer_experiment.py -i $input $INFEREXPERIMENT_FLAGS > $output
""","inferexperiment"
Bpipe From line 19 of RNAseq/inferexperiment.groovy 
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exec """

    ${PREAMBLE} &&

    for i in `cut -f2 $PRERMATS_vars.contrasts | sort | uniq`; do 
        if [[ "\${i}" == "contrast" ]];
        then
           echo "Skipping header line of contrasts file\n";
           continue;
        fi;
        contrast=\${i:1:-1};
        groups[0]=`echo \${i:1:-1} | cut -d- -f1`;
        groups[1]=`echo \${i:1:-1} | cut -d- -f2`;
        groups=`echo \${groups[0]} \${groups[1]}`;
        echo \${groups};
        awk -v G="\$groups" 'BEGIN {OFS="\t"}{ split(G, g, / /)} { if( \$3 == g[1] || \$3 == g[2] ) { split(\$2,f,"."); \$2=f[1]; print \$0 } }' $PRERMATS_vars.targets > $output.dir/\${contrast}_targets_rMATS.txt;
    done
""", "PRERMATS"
Bpipe From line 49 of RNAseq/prermats.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    unset DISPLAY;
    echo $output.prefix;
    qualimap rnaseq -bam $input -outdir ${output.prefix}_qualimap -outformat html -gtf ${qualimap_vars.genesgtf} -oc $output -p ${qualimap_vars.protocol} ${qualimap_vars.extra}
""","qualimap"
Bpipe QualiMap From line 25 of RNAseq/qualimap.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    input_var=`basename $input`;
    suffix=${rMATS_vars.suffix};
    groups=\${input_var%\$suffix};
    echo "groups after suffix removal" \$groups;
    sep=${rMATS_vars.sep};
    groups=(\${groups//\$sep/ });
    echo "groups 0 " \${groups[0]};
    add_extensions="";
    if [[ "$RUN_CUTADAPT" == "true" ]]; then
        echo "Will add cutadapt extension";
        add_extensions=".cutadapt";
    fi;
    echo \${add_extensions};
    mkdir -p $output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS &&
    bamgroup0=`awk -v g="\${groups[0]}" -v M="$MAPPED" -v C="\${add_extensions}" 'BEGIN{OFS=""} {if (\$3 == g) print M "/" \$2 C ".bam"}' $input | paste -sd, -` &&
    echo \$bamgroup0 > $output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS/\${groups[0]}_samples.txt &&
    bamgroup1=`awk -v g="\${groups[1]}" -v M="$MAPPED" -v C="\${add_extensions}" 'BEGIN{OFS=""} {if (\$3 == g) print M "/" \$2 C ".bam"}' $input | paste -sd, -` &&
    echo \$bamgroup1 > $output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS/\${groups[1]}_samples.txt &&
    run_rmats --b1 $output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS/\${groups[0]}_samples.txt --b2 $output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS/\${groups[1]}_samples.txt $RMATS_FLAGS --od $output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS --tmp $output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS_tmp && 
    Rscript ${PIPELINE_ROOT}/tools/maser/createMaserPlots.R $MASER_FLAGS rmats_dir=$output.dir/\${input_var%${rMATS_vars.suffix}}_rMATS scripts_dir=${PIPELINE_ROOT}/tools/maser group1=\${groups[0]} group2=\${groups[1]} &&

    rm -rf $output.dir/*_tmp/ &&

    touch $output;
""","rMATS"
Bpipe Cutadapt From line 50 of RNAseq/rmats.groovy 
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       exec """
           ${PREAMBLE} &&

           cp ${PIPELINE_ROOT}/tools/reports/shiny_rnaseq_reporting_tool/DE.shinyrep.helpers.R ${REPORTS}   &&
           cp ${PIPELINE_ROOT}/tools/reports/shiny_rnaseq_reporting_tool/styles.css ${REPORTS}              &&

           if [ -e "${REPORTS}/DEreport.Rmd" ]; then
               echo 'DEreport.Rmd already exists. Older copy will be kept and not overwritten';
           else
               cp ${PIPELINE_ROOT}/tools/reports/shiny_rnaseq_reporting_tool/DEreport.Rmd ${REPORTS};
           fi &&

           PROJECT=\$(basename ${shinyReports_vars.project})                    &&
           sed -i "2,2s/SHINYREPS_PROJECT/\${PROJECT}/" ${REPORTS}/DEreport.Rmd &&

           echo "SHINYREPS_PROJECT=${shinyReports_vars.project}" >  $output &&
           echo "SHINYREPS_ORG=${shinyReports_vars.org}"         >> $output &&
           echo "SHINYREPS_DB=${shinyReports_vars.db}"           >> $output &&
           echo "SHINYREPS_LOG=${shinyReports_vars.log}"         >> $output &&
           echo "SHINYREPS_PAIRED=${shinyReports_vars.paired}"   >> $output &&
           echo "SHINYREPS_QC=${shinyReports_vars.qc}"           >> $output &&
           echo "SHINYREPS_RES=${shinyReports_vars.res}"         >> $output &&
           echo "SHINYREPS_PREFIX=${shinyReports_vars.prefix}"   >> $output &&
           echo "SHINYREPS_STRANDEDNESS=${shinyReports_vars.strandedness}" >> $output &&
           echo "SHINYREPS_STAR_LOG=${shinyReports_vars.star_log}"       >> $output &&
           echo "SHINYREPS_STAR_SUFFIX=${shinyReports_vars.star_suffix}" >> $output &&
           echo "SHINYREPS_STARparms_SUFFIX=${shinyReports_vars.starparms_suffix}" >> $output &&
           echo "SHINYREPS_FASTQC_OUT=${shinyReports_vars.fastqc_out}"     >> $output &&
           echo "SHINYREPS_FASTQC_LOG=${shinyReports_vars.fastqc_log}"     >> $output &&
           echo "SHINYREPS_FASTQC_SUMMARIZED=${shinyReports_vars.fastqc_summarized}" >> $output &&
           echo "SHINYREPS_FASTQSCREEN_OUT=${shinyReports_vars.fastqscreen_out}" >> $output &&
           echo "SHINYREPS_FASTQSCREEN_LOG=${shinyReports_vars.fastqscreen_log}" >> $output &&
           echo "SHINYREPS_FASTQSCREEN_PERC=${shinyReports_vars.fastqscreen_perc}" >> $output &&
           echo "SHINYREPS_RUN_CUTADAPT=${shinyReports_vars.run_cutadapt}"  >> $output &&
	    echo "SHINYREPS_CUTADAPT_STATS=${shinyReports_vars.cutadapt_stats}" >> $output &&
           echo "SHINYREPS_BAMINDEX_LOG=${shinyReports_vars.bamindex_log}"     >> $output &&
           echo "SHINYREPS_DUPRADAR_LOG=${shinyReports_vars.dupradar_log}" >> $output &&
           echo "SHINYREPS_RNATYPES_LOG=${shinyReports_vars.rnatypes_log}" >> $output &&
           echo "SHINYREPS_RNATYPES=${shinyReports_vars.rnatypes}" >> $output &&
           echo "SHINYREPS_RNATYPES_SUFFIX=${shinyReports_vars.rnatypes_suffix}" >> $output &&
           echo "SHINYREPS_GENEBODYCOV_LOG=${shinyReports_vars.genebodycov_log}" >> $output &&
           echo "SHINYREPS_DE_DESEQ=${shinyReports_vars.de_deseq}"       >> $output &&
           echo "SHINYREPS_DE_DESEQ_MM=${shinyReports_vars.de_deseq_mm}" >> $output &&
           echo "SHINYREPS_DE_DESEQ_FDR=${shinyReports_vars.de_deseq_FDR}"       >> $output &&
           echo "SHINYREPS_DE_DESEQ_FC=${shinyReports_vars.de_deseq_FC}"       >> $output &&
           echo "SHINYREPS_MASER_SCRIPTS=${shinyReports_vars.maser_scripts}" >> $output &&
           echo "SHINYREPS_MASER_FTYPE=${shinyReports_vars.maser_ftype}" >> $output &&
           echo "SHINYREPS_MASER_MINCOV=${shinyReports_vars.maser_mincov}" >> $output &&
           echo "SHINYREPS_MASER_FDR=${shinyReports_vars.maser_fdr}" >> $output &&
           echo "SHINYREPS_MASER_DPSI=${shinyReports_vars.maser_dpsi}" >> $output &&
           echo "SHINYREPS_SUBREAD=${shinyReports_vars.subread}"         >> $output &&
           echo "SHINYREPS_SUBREAD_SUFFIX=${shinyReports_vars.subread_suffix}"  >> $output &&
           echo "SHINYREPS_SUBREAD_LOG=${shinyReports_vars.subread_log}"        >> $output &&
           echo "SHINYREPS_BAM2BW_LOG=${shinyReports_vars.bam2bw_log}"          >> $output &&
           echo "SHINYREPS_MARKDUPS_LOG=${shinyReports_vars.markdups_log}"      >> $output &&
           echo "SHINYREPS_DESEQ_LOGS=${shinyReports_vars.deseq_logs}"          >> $output &&
           echo "SHINYREPS_PLOTS_COLUMN=${shinyReports_vars.plots_column}"      >> $output &&
           echo "SHINYREPS_SORT_ALPHA=${shinyReports_vars.sort_alpha}"          >> $output &&
           echo "SHINYREPS_INFEREXPERIMENT_LOGS=${shinyReports_vars.inferexperiment_logs}" >> $output &&
           echo "SHINYREPS_QUALIMAP_LOGS=${shinyReports_vars.qualimap_logs}" >> $output &&
           echo "SHINYREPS_INSERTSIZE=${shinyReports_vars.insertsize}" >> $output &&
           echo "SHINYREPS_GO_ENRICHMENT=${shinyReports_vars.go_enrichment}" >> $output &&
           echo "SHINYREPS_TRACKHUB_DONE=${shinyReports_vars.trackhub_done}" >> $output &&
           echo "SHINYREPS_TOOL_VERSIONS=${shinyReports_vars.tool_versions}" >> $output &&
           echo "SHINYREPS_TARGET=${shinyReports_vars.target}" >> $output
       ""","shinyReports"
Bpipe From line 13 of RNAseq/shinyreports.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    if [ -e \${TMP}/$OUTPUTFILE ]; then
        echo 'removing old STAR tmp folder';
        rm -r \${TMP}/$OUTPUTFILE*;
    fi &&

    STAR $STAR_FLAGS --outTmpDir \${TMP}/$OUTPUTFILE --readFilesIn $inputs | samtools view $SAMTOOLS_VIEW_FLAGS - | samtools sort $SAMTOOLS_SORT_FLAGS -T \${TMP}/${OUTPUTFILE}_sort - > $output1 &&

    mv ${STAR_vars.logdir}/${OUTPUTFILE}SJ.out.tab $output.dir &&
    ln -s ${STAR_vars.logdir}/${OUTPUTFILE}Log.final.out $output.dir
""","STAR"
Bpipe SAMtools STAR From line 54 of RNAseq/star.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    base=`basename $input` &&
    if [[ "${subread2rnatypes_vars.paired}" == "true" ]]; then            
        echo "We are resorting and doing the repair\n" &&
        repair -i $input -T ${subread2rnatypes_vars.threads} -o \${TMP}/\${base} &&
        featureCounts $RNATYPES_FLAGS -o \${TMP}/\${base} \${TMP}/\${base} 2> ${output.prefix}_rnatypeslog.stderr;
    else
        featureCounts $RNATYPES_FLAGS -o \${TMP}/\${base} $input 2> ${output.prefix}_rnatypeslog.stderr;
    fi &&
    cut -f1,6,7 \${TMP}/\${base} > $output &&
    rm \${TMP}/\${base}
""","subread2rnatypes"
Bpipe FeatureCounts From line 25 of RNAseq/subread2rnatypes.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

    base=`basename $input` &&
    if [[ "${subread_count_vars.paired}" == "true" ]]; 
    then
        echo "We are resorting and doing the repair\n" &&
        repair -i $input -T ${subread_count_vars.threads} -o \${TMP}/\${base} &&
        featureCounts $SUBREAD_FLAGS -o $output \${TMP}/\${base} 2> ${output.prefix}_subreadlog.stderr;
    else
        featureCounts $SUBREAD_FLAGS -o $output $input 2> ${output.prefix}_subreadlog.stderr;
    fi
""","subread_count"
Bpipe FeatureCounts From line 23 of RNAseq/subread.groovy 
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exec """
    ${TOOL_ENV} &&
    ${PREAMBLE} &&

     Rscript ${PIPELINE_ROOT}/tools/TPMs/TPMs.R -c $input -o $output $TPM_FLAGS

""","tpm"
Bpipe From line 19 of RNAseq/tpm.groovy
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Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://gitlab.rlp.net/imbforge/NGSpipe2go/-/tree/master/pipelines/RNAseq
Name: rna-seq
Version: Version 1
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Other Versions:
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Downloaded: 0
Copyright: Public Domain
License: None
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ncov_2
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Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
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snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
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ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
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RNA-seq workflow using STAR and DESeq2
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public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
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This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57