Discover published sets by community

Primary Use: Manipulating high-throughput sequencing (HTS) data and formats. Example Command: java -jar picard.jar SortVcf I=input.vcf O=sorted.vcf

Primary Use: Microbial community analysis from raw DNA sequencing data. Example Command: qiime demux emp-single --i-seqs emp-single-end-sequences.qza --m-barcodes-file sample-metadata.tsv --m-barcodes-column BarcodeSequence --o-per-sample-sequences demux

Primary Use: Variant discovery in high-throughput sequencing data. Example Command: gatk HaplotypeCaller -R reference.fa -I input.bam -O output.vcf

Primary Use: Assigning taxonomic labels to short DNA sequences with high accuracy. Example Command: kraken --db minikraken_20171019_8GB --fastq-input input.fastq --output output.txt --report report.txt

Primary Use: Analysis and comprehension of high-throughput genomic data. Example Command: source('https://bioconductor.org/biocLite.R'); biocLite('GenomicFeatures')

Primary Use: Quality control for high throughput sequence data. Example Command: fastqc input.fastq -o output_dir

Primary Use: A powerful toolset for genome arithmetic. Example Command: bedtools intersect -a fileA.bed -b fileB.bed > output.bed

Primary Use: Manipulating alignments in the SAM format. Example Command: samtools view -bS input.sam > output.bam

Primary Use: Fast and memory-efficient tool for aligning sequencing reads to long reference sequences. Example Command: bowtie2 -x genome_index -U reads.fq -S output.sam

Primary Use: Aligning sequences to a reference genome. Example Command: hisat2 -x genome_index -f -U input.fasta -S output.sam

Primary Use: Finding regions of local similarity between sequences. Example Command: blastn -query input.fasta -db nt -out results.out

Primary Use: Transcriptome assembly and differential expression analysis for RNA-Seq. Example Command: cufflinks -p 8 -o output_dir input.bam

Primary Use: Multiple sequence alignment. Example Command: mafft --auto input.fasta > output.fasta

Primary Use: Multiple sequence alignment program for protein and nucleotide sequences. Example Command: muscle -in input.fa -out output.fa

Primary Use: Multiple sequence alignment. Example Command: clustalo -i input.fasta -o output.fasta -v

Primary Use: Variant annotation and effect prediction tool. Example Command: java -Xmx4g -jar snpEff.jar eff -v genome.versions input.vcf > output.vcf

Primary Use: Tool designed for QC, analysis, and exploration of single-cell RNA-seq data. Example Command: Seurat::CreateSeuratObject(raw.data = raw.data)

Primary Use: Aligning RNA-Seq reads to a genome in order to identify splice junctions. Example Command: tophat2 -p 8 -G genes.gtf -o output genome_index reads.fq

Primary Use: Enables accessible, reproducible, and transparent computational research. Example Command: Through a web interface rather than command line.