Name,Tool,Description,Step,Category
Bowtie2,<a href='http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml'>Bowtie2</a>,Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.,Alignment,1
bwa,<a href='http://bio-bwa.sourceforge.net/bwa.shtml'>bwa</a>,"BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. ",Alignment,1
Gsnap,<a href='http://research-pub.gene.com/gmap/'>Gsnap</a>,GSNAP is a genomic short-read nucleotide alignment program.,Alignment,1
Hisat2,<a href='https://ccb.jhu.edu/software/hisat2/manual.shtml'>Hisat2</a>,HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) to reference genomes.,Alignment,1
Rsubread,<a href='https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf'>Rsubread</a>,Rsubread is a Bioconductor software package that provides high-performance alignment and read counting functions for RNA-seq reads.,Alignment,1
STAR,<a href='https://github.com/alexdobin/STAR'>STAR</a>,STAR is an ultrafast universal RNA-seq aligner.,Alignment,1
Tophat2,<a href='https://ccb.jhu.edu/software/tophat/manual.shtml'>Tophat2</a>,TopHat is a fast splice junction mapper for RNA-Seq reads.,Alignment,1
Bismark,<a href='https://www.bioinformatics.babraham.ac.uk/projects/bismark/'>Bismark</a>,Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.,Bisulfite mapping,2
Trinity,<a href='https://github.com/trinityrnaseq/trinityrnaseq/wiki'>Trinity</a>,Trinity assembles transcript sequences from Illumina RNA-Seq data.,denovo Transcriptome Assembly,3
TransDecoder,<a href='https://github.com/TransDecoder/TransDecoder/wiki'>TransDecoder</a>,TransDecoder identifies candidate coding regions within transcript sequences.,Find Coding Regions,4
Picard,<a href='https://broadinstitute.github.io/picard/'>Picard</a>,Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.,Manipulating HTS data,5
Blast,<a href='https://www.ncbi.nlm.nih.gov/books/NBK279690/'>Blast</a>,BLAST finds regions of similarity between biological sequences.,Blast,13
MACS2,<a href='https://macs3-project.github.io/MACS/'>MACS2</a>,MACS2 identifies transcription factor binding sites in ChIP-seq data.,Peak calling,6
Samtools,<a href='http://www.htslib.org/doc/samtools-1.2.html'>Samtools</a>,Samtools is a suite of programs for interacting with high-throughput sequencing data.,Post-processing,7
Busco,<a href='https://busco.ezlab.org/'>Busco</a>,BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.,Quality,8
Fastqc,<a href='https://www.bioinformatics.babraham.ac.uk/projects/fastqc/'>Fastqc</a>,FastQC is a quality control tool for high throughput sequence data.,Quality,8
TransRate,<a href='http://hibberdlab.com/transrate/'>TransRate</a>,Transrate is software for de-novo transcriptome assembly quality analysis.,Quality,8
Kallisto,<a href='https://pachterlab.github.io/kallisto/manual'>Kallisto</a>,kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.,Read counting,9
FASTX-Toolkit,<a href='http://hannonlab.cshl.edu/fastx_toolkit/commandline.html'>FASTX-Toolkit</a>,FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.,Read Preprocessing,10
Trim_galore,<a href='https://github.com/FelixKrueger/TrimGalore'>Trim_galore</a>,Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files.,Read Preprocessing,10
Trimmomatic,<a href='http://www.usadellab.org/cms/?page=trimmomatic'>Trimmomatic</a>,Trimmomatic is a flexible read trimming tool for Illumina NGS data.,Read Preprocessing,10
Trinotate,<a href='https://github.com/Trinotate/Trinotate.github.io/wiki'>Trinotate</a>,Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes.,Transcriptome Functional Annotation,11
BCFtools,<a href='https://samtools.github.io/bcftools/howtos/index.html'>BCFtools</a>,BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.,Variant Discovery,12
GATK,<a href='https://gatk.broadinstitute.org/hc/en-us'>GATK</a>,Variant Discovery in High-Throughput Sequencing Data.,Variant Discovery,12
