Man pages for GrahamHamilton/pipelineTools
Pipeline Tools for NGS Sequence Analysis Pipelines
| prepare_samples | Prepare samples |
| prepare_solo_samples | Title |
| run_bcftools | Run bcftools |
| run_bedtools | Run the Bedtools program |
| run_blast | Run BLAST programs |
| run_bowtie | Run bowtie |
| run_bowtie2 | Run the Bowtie2 |
| run_bwa | Run the BWA aligner |
| run_centrifuge | Run Centrifuge |
| run_cutadapt | Run Cutadapt |
| run_cuteSV | Run cuteSV |
| run_deeptools | Run Deeptools |
| run_fastp | Run FastP |
| run_fastqc | Run FastQC |
| run_fastq_screen | Run Fastq-Screen |
| run_flye | Run the Flye assembler |
| run_freebayes | Run Freebayes |
| run_gatk | Run GATK |
| run_hisat2 | Run HISAT2 |
| run_htseq_count | Run HtSeq-Count |
| run_kallisto | Run Kallisto |
| run_macs | Run Macs3 |
| run_mageck | Run Mageck |
| run_masurca | Run the MaSuRCA assembly program |
| run_minimap2 | Run Minimap2 |
| run_multiqc | Run MultiQC |
| run_nanofilt | Run the NanoFilt program |
| run_picard | Run Picard |
| run_samtools | Run Samtools |
| run_seqtk | Run Seqtk |
| run_sicer | Run Sicer2 |
| run_snpeff | Run SnpEff |
| run_snpsift | Run SnpSift |
| run_star | Run the STAR/STARsolo program |
| run_stringtie | Run Stringtie |
| run_umitools | Run UMITools |
| run_vcf_index | Compress and index vcf files |
| run_vcftools | Run vcftools |
| save_pheatmap_png | Save pheatmap |
