Man pages for GrahamHamilton/pipelineTools
Pipeline Tools for NGS Sequence Analysis Pipelines

prepare_samplesPrepare samples
run_bcftoolsRun bcftools
run_bedtoolsRun the Bedtools program
run_blastRun BLAST programs
run_bowtieRun bowtie
run_bowtie2Run the Bowtie2
run_bwaRun the BWA aligner
run_centrifugeRun Centrifuge
run_cutadaptRun Cutadapt
run_cuteSVRun cuteSV
run_deeptoolsRun Deeptools
run_fastpRun FastP
run_fastqcRun FastQC
run_fastq_screenRun Fastq-Screen
run_flyeRun the Flye assembler
run_freebayesRun Freebayes
run_gatkRun GATK
run_hisat2Run HISAT2
run_htseq_countRun HtSeq-Count
run_kallistoRun Kallisto
run_macsRun Macs3
run_mageckRun Mageck
run_minimap2Run Minimap2
run_multiqcRun MultiQC
run_nanofiltRun the NanoFilt program
run_picardRun Picard
run_samtoolsRun Samtools
run_sicerRun Sicer2
run_snpeffRun SnpEff
run_snpsiftRun SnpSift
run_starRun the STAR/STARsolo program
run_stringtieRun Stringtie
run_umitoolsRun UMITools
run_vcf_indexCompress and index vcf files
run_vcftoolsRun vcftools
save_pheatmap_pngSave pheatmap
GrahamHamilton/pipelineTools documentation built on Feb. 19, 2024, 1:03 a.m.