Snakemake wrappers for bioinformatics research.
| Tool | Description |
| Differential expression | |
| DESeq2 | |
| EBSeq | |
| edgeR | |
| Gene expression quantification | |
| rsem | |
| feature-counts | |
| htseq | |
| kallisto | |
| cufflinks | |
| salmon | |
| Working with PDB files | |
| fetch-pdb | Fetch pdb file from RCSB PDB using PDB ID. |
| fetch-pdb-fasta | Fetch FASTA sequence associated with PDB ID. |
| Variant calling | |
| freebayes | |
| somatic-sniper | |
| varscan/somatic | |
| strelka2 | |
| Variant annotation | |
| snpeff | |
| Copy number analysis | |
| varscan/copynumber | |
| varscan/copycaller | |
| dnacopy/cbs-segmentation | |
| cnvkit | |
| Sequencing data retrieval | |
| sra-tools | |
| prefetch | |
| parallel-fastq-dump | |
| Sequencing read preprocessing | |
| fastqc | The most popular quality-control tool for high-throughput sequencing data. |
| trim-galore | Adapter trimming and quality control. Also provides RRBS-specific trimming option. |
| fastp | |
| Sequencing read alignment | |
| bwa | |
| bowtie | |
| bowtie2 | |
| Splice-aware sequencing read alignment | |
| hisat2 | |
| star | |
| Bisulfite-treated sequencing read alignment | |
| bismark | |
| bwa-meth | |
| bsmap | |
| Alignment manipulation | |
| sambamba | A faster alternative of samtools. Wrappers for Sort, Index, Merge, Flagstat, Markdup are implemented for now. |
| samtools | Manipulates Sequence Alignment/Map (SAM) format. Wrappers for Sort, Index, Faidx are implemented for now. |
| Bisulfite-seq postprocessing | |
| methyldackel | |
| Miscellaneous | |
| subsample-fastq | |
| wgsim | |
| tabix | |
| igvtools | |