Server
OS
Ubuntu 24.04 LTS
CPU cores
8
RAM
31Gi
Disk (total)
5.4T
Disk (free)
5.0T
Python
3.11.15
R
4.3.3
Last updated
2026-04-28 12:06 UTC
Alignment & Mapping
BWA
Burrows-Wheeler Aligner
BWA-MEM2
Faster BWA for modern CPUs
Bowtie2
Fast short-read aligner
HISAT2
Splice-aware RNA/DNA aligner
STAR
Spliced Transcripts Alignment
minimap2
Long-read & splice aligner
subread
Subread aligner
Quality Control & Trimming
FastQC
Per-base sequence quality
MultiQC
Aggregate QC reports
fastp
Ultra-fast FASTQ preprocessor
Trimmomatic
Flexible read trimmer
Trim Galore
Trim + FastQC wrapper
Falco
Fast FastQC alternative
samtools
SAM/BAM/CRAM processing
picard
Broad SAM/BAM toolkit
sambamba
Fast samtools alternative
mosdepth
Fast coverage depth
Variant Calling
GATK4
Genome Analysis Toolkit
bcftools
Variant calling & manipulation
FreeBayes
Bayesian variant caller
Structural Variants & Copy Number
Manta
SV caller (Illumina) — Docker
DELLY
SV discovery paired-end
CNVkit
Copy number variation toolkit
mosdepth
Depth of coverage
Annotation
SnpEff
Variant annotation & effect
vcfanno
Annotate VCF with any file
RNA-seq & Expression
Kallisto
Pseudoalignment quantification
Salmon
Transcript quantification
StringTie
Transcript assembly & quant
HISAT2
Splice-aware RNA aligner
STAR
RNA-seq aligner
Methylation
Bismark
Bisulfite mapping & extraction
Long Reads
minimap2
Long-read aligner
NanoStat
Nanopore read statistics
Chopper
Nanopore quality filtering
seqtk
Sequence toolkit
Assembly
SPAdes
De novo genome assembler
Flye
Long-read assembler
Metagenomics
Kraken2
Taxonomic classification
Bracken
Abundance re-estimation
Diamond
Fast protein alignment
Utilities
bedtools
Genome arithmetic
seqkit
FASTA/Q toolkit
vcftools
VCF file processing
PLINK2
GWAS analysis toolkit
SRA-tools
NCBI SRA download tools
Entrez-Direct
NCBI Entrez CLI
pigz
Parallel gzip
GNU parallel
Shell job parallelisation
Workflow Managers
Nextflow
DSL2 pipeline framework
Snakemake
Python-based workflow manager
R & Bioconductor
DESeq2
Differential expression for count data
edgeR
Differential expression (NB model)
limma
Linear models for omics data
GenomicRanges
Genomic interval manipulation
Biostrings
Biological sequence manipulation
Rsamtools
BAM/SAM file interface
rtracklayer
Import/export genomic tracks
AnnotationHub
Bioc annotation resources
biomaRt
Ensembl BioMart interface
SingleCellExperiment
Single-cell infrastructure
scran
Single-cell normalisation
VariantAnnotation
VCF parsing & annotation
minfi
DNA methylation arrays
ChIPseeker
ChIP-seq peak annotation
DiffBind
Differential binding analysis
clusterProfiler
Gene ontology & enrichment
ComplexHeatmap
Complex heatmap visualisation
EnhancedVolcano
Publication volcano plots
Gviz
Genomic data visualisation