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snakemake-wrappers

pipe

Snakemake wrappers for bioinformatics research.

Available wrappers

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