dnaseq.py -t mpileup
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Skewer trimming .bam .fastq 3 Bwa mem picard sort sam 10 sym link final bam 8 Picard mark duplicates 9 Recalibration 7 Fix mate by coordinate 6 Sambamba merge realigned 5 Gatk indel realigner 4 Sambamba merge sam files 11 Metrics dna picard metrics 15 Picard calculate hs metrics 14 Metrics dna fastqc 13 Metrics dna sambamba flagstat 12 Metrics dna sample qualimap 16 Gatk callable loci 18 Baf plot 17 Extract common snp req 30 Run multiqc 29 Mpileup metrics snv graph metrics 21 snp and Indel bcf 20 Rawmpileup cat 19 Rawmpileup 26 Mpileup snp effect 25 Mpileup snp id annotation 24 mpileup flag mappability 23 Mpileup filter nstretches 22 Merge filter bcf 28 Mpileup metrics vcf stats 27 Mpileup dbnsfp annotation
Figure S1
dnaseq_high_coverage.py
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Trimmomatic 3 Merge trimmomatic Stats 4 Picard merge sam files .bam .fastq 5 Gatk indel realigner 10 Gatk callable loci 9 Picard calculate hs metrics 8 Metrics 7 Picard fixmate 6 Merge realigned 12 Preprocess vcf 11 Call variants 14 Gemini annotations 13 Snp effect
Figure S2
rnaseq.py
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Trimmomatic 3 Merge trimmomatic Stats .bam .fastq 4 Star 25 Verify Bam ID 24 IHEC metrics 23 Differential expression GOseq 22 Differential expression 21 GQ seq utils exploratory analysis RNAseq 20 FPKM corrolation matrix 19 Cuffnorm 18 Cuffdiff 17 CuffQuant 16 Cuffmerge 15 Cufflinks 14 Raw counts metrics 13 Raw counts 12 Wiggle 11 RNASeQC 10 Bam hard clip 9 Estimate ribosomal RNA 8 Picard RNA metrics 7 Picard mark duplicates 6 Picard Sort Sam 5 Picard merge Sam files
Figure S3
rnaseq_light.py
Step per readset File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Trimmomatic 3 Merge trimmomatic Stats .bam .fastq 4 Kallisto 6 Gq seq utils exploratory analysis rnaseq light 5 Kallisto count matrixFigure S4
rnaseq_denovo_assembly.py
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Trimmomatic 3 Merge trimmomatic Stats 4 Insilico read normalization readsets .bam .fastq 5 Insilico read normalization all 6 Trinity 8 Blastx trinity uniprot 9 Blastx trinity uniprot merge 10 Transdecoder 11 Hmmer 12 Rnammer transcriptome 13 Blastp transdecoder uniprot 14 Signalp 15 Tmhmm 16 Trinotate 17 Align and estimate abundance prep reference 18 Align and estimate abundance 19 Gq seq utils exploratory analysis rnaseq denovo 20 differential expression 21 filter annotated components 22 Gq seq utils exploratory analysis rnaseq denovo filtered 23 differential expression filtered 7 Exonerate fastasplit
Figure S5
chipseq.py
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Trimmomatic 3 Merge trimmomatic Stats 4 bwa mem Picard sort sam .bam .fastq 5 Samtools view filter 18 IHEC metrics 17 Run SPP 16 IHEC preprocess files 15 Annotation graphs 14 Homer find motifs genome 13 HOMER annotate peaks 12 MACS2 call peaks 11 Homer make UCSC file 19 MultiQC report 10 QC metrics 9 Homer make tag directory 8 Metrics 7 Picard mark duplicates 6 Picard merge sam files
Figure S6
tumor_pair.py -t sv
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Skewer trimming .bam .fastq 3 Bwa mem picard sort sam 18 Ensemble metasv 17 Svaba assemble 16 Scones 15 cnvkit batch 14 Wham call sv 13 Lumpy paired sv 12 Manta sv calls 11 Delly call filter 10 sCNAphase 9 Sequenza 8 Recalibration 7 Sambamba mark duplicates 6 Sambamba merge realigned 5 Gatk indel realigner 4 Sambamba merge sam files
Figure S7
tumor_pair.py -t ensemble
1 Picard Sam to Fastq 2 Skewer trimming .bam .fastq 3 Bwa mem picard sort sam 33 Sample Gemini annotations germline 32 Compute cancer effects germline 31 Merge Gatk variant annotator germline 27 Compute cancer effects somatic 26 Merge Gatk variant annotator somatic 23 Merge filter paired vardict 22 Vardict paired 21 Merge filter paired samtools 20 Samtools paired 19 Merge Mutect2 18 paired Mutect2 14 run pair Multiqc 9 Conpair concordance contamination 8 Recalibration 7 Sambamba mark duplicates 6 Sambamba merge realigned 5 Gatk indel realigner 4 Sambamba merge sam files 30 Gatk variant annotator germline 25 Gatk variant annotator somatic 15 Rawmpileup 13 metrics dna fastqc 12 Metrics dna Sambamba flagstat 11 Metrics dna sample qualimap 10 Metrics dna Picard metrics 28 Sample Gemini annotations somatic 17 Merge Varscan2 16 paired Varscan2 29 Ensemble germline loh 24 Ensemble somaticStep per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency
Figure S8
tumor_pair.py -t fastpass
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Skewer trimming .bam .fastq 3 Bwa mem picard sort sam 18 Run pair Multiqc 17 Metrics dna fastqc 16 Metrics dna sambamba flagstat 15 Metrics dna sample qualimap 14 Metrics dna picard metrics 13 Gemini annotations panel 12 SNP effect panel 11 Preprocess vcf panel 10 Merge Varscan2 panel 9 Paired Varscan2 panel 8 Rawmpileup panel 7 Sambamba mark duplicates 6 Sambamba merge realigned 5 Gatk indel realigner 4 Sambamba merge sam files
Figure S9
methylseq.py
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Picard Sam to Fastq 2 Trimmomatic 3 Merge trimmomatic Stats .bam .fastq 4 Bismark Align 13 IHEC sample metrics report 12 All sample metric report 11 Methylation profile 14 Bis SNP 10 Wiggle tracks 9 Methylation call 8 Verify bam ID 7 Metrics 6 Picard remove duplicates 5 Picard merge sam files
Figure S10
7 Samtools merge bams 1 Samtools bam sort 2 Picard Sam to Fastq 3 Trimmomatic 4 Merge Trimmomatic Stats 5 Fastq ReadName Edit 6 HiCUP align 8 HOMER tag directory 13 Identify TADs RobusTAD 12 Identify TADs TopDom 15 Create .hic file 9 Interaction matrices Chr 10 Interaction matrices genome 11 Identify compartments 14 Identify peaks 16 MultiQC Report .bam .fastq Timmomatic Stats HICUP report HOMER R plots
hicseq.py -t hic
.hicStep per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency
Figure S11
7 Samtools merge bams 1 Samtools bam sort 2 Picard Sam to Fastq 3 Trimmomatic 4 Merge trimmomatic Stats 5 Fastq ReadName Edit 6 HiCUP align 8 Create rmap file 16 Create .hic file 17 MultiQC Report .bam .fastq Timmomatic Stats HICUP report
hicseq.py -t capture
.hic 9 Create baitmap file 10 Create design files 11 Create input files 12 Run CHICAGO 13 Run CHICAGO featureOverlap 14 Bait Intersect Capture15 Intersect Genome Digest Capture .bedStep per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency
Figure S12
ampliconseq.py
Step per readset
File Input/output Step on multiple readsets/samples Alternative entry Step dependency 1 Trimmomatic 2 Merge trimmomatic Stats .fastq 3 Flash 20 Qiime report2 19 Sample rarefaction plot 18 Collate alpha 9 OTU rep picking 8 OTU picking 7 Merge uchime stats 6 uchime 5 Catenate 4 Merge flash stats 11 OTU table 10 OTU assigning 13 Filter alignment 12 OTU alignment 15 Qiime report 14 Phylogeny 20 Qiime report2 19 Sample rarefaction plot 18 Collate alpha 17 Alpha diversity 16 Multiple rarefaction 26 Plot heatmap 25 Plot taxa 24 Summarize taxa 23 Rarefaction plot 22 Css normalization 21 Single rarefaction 28 Plot to alpha 27 Krona 32 Plot to beta 31 Pcoa plot 30 Pcoa 29 Beta diversity
Figure S13
pacbio_assembly.py
Step per readset
File Input/output Alternative entry Step dependency 1 Smrtanalysis filtering 2 PacBio tools get cutoff bax.h5 3 Preassembly 4 Assembly 5 Polishing 6 PacBio tools assembly stats 9 Compile 10 Circlator 7 Blast 8 Mummer 11 Base Modification 12 Motif Maker
