Bioinformatic tools & resources


  • NGS tools

fastqca quality control tool for high throughput sequence data.

samtools - processing sequence alignments in SAM and BAM formats -

sickle -

seqtk -

sra-toolkit - The toolkit library provides the mechanism for inserting and search for information in the SRA database.

snpeff - It's a SNP effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions and deletions) on genes.

bedtools - The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.

bamtools - BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

casava -

fastx-toolkit - The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

picard-tools - Picard comprises Java-based command-line utilities that manipulate SAM files


  • Alignment

Bowtie - Bowtie is an ultrafast, memory-efficient short read aligner.

Bwa - Burrows-Wheeler Aligner

Soap - SOAP is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences.

Blastall -

Blat -

ClustalW - global multiple nucleotide or peptide sequence alignment

ClustalX - Multiple alignment of nucleic acid and protein sequences (graphical interface)

t-coffee - Multiple Sequence Alignment

blastz - blastz alignment program


  • Assembly

Velvet  - Nucleic acid sequence assembler for very short reads

tigra-sv -

CAP3 - CAP3 Assembly Program

Trinity (inchworm, cryalis, butterfly) - The inchworm RNA-Seq assembler, developed at the Broad Institute, employs the Kmer graph method

                                                                                to reconstruct (in many cases full-length) transcripts from Illumina RNA-Seq (preferrably strand-specific)

                                                                                reads. Inchworm is especially effective when used with strand-specific RNA-Seq data.

Soap-denovo -

Trans-Abyss -


  • Genome and variation analysis

cgatools - Tools developed by Complete genomics,  somatic, de novo variation calls,


samtools - processing sequence alignments in SAM and BAM formats

gatks -

Varscan2 -

snvmix2 - Detecting single nucleotide variants from next generation sequencing data

somaticsniper -

polyphen2 -

provean -

JoinSNVMix -

Breakdancer - BreakDancerMax predicts five types of structural variants:


tea -

meerkat -



  • RNA-seq analysis

Tophat - TopHat is a fast splice junction mapper for RNA-Seq reads.

Cufflinks - Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples.


edgeR -  Empirical analysis of digital gene expression  data in R




  • RNA analysis



Sylamer - Motif enrichment analysis with fold changes of RNAs (

mirdeep - The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...).


  • lncRNAs

Cpc -

RNACode - RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences.