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ABBLAST Basic Local Alignment Search Tool from Advanced Biocomputing, LLC


ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.



A new short read genome assembler from the Computational Research and Development group at the Broad Institute.



The BAM format is an efficient method for storing and sharing data from modern, highly parallel sequencers. While primarily used for storing alignment information, BAMs can (and frequently do) store unaligned reads as well.


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


BIOPERL Bioperl is a collection of perl libraries that ease common bioinformatic needs and integrate with common file formats.


BLAST+ Basic Local Alignment Search Tool is the most frequently used sequence homology search tool.


BLAST Basic Local Alignment Search Tool is the most frequently used sequence homology search tool.


Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).



BWA Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW.


Celera Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.


DSSP DSSP is a database of secondary structure assignments for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries.


Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.


FASTA FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.


FASTQC is a quality control tool for high throughput sequence data.


FASTX-TOOLKIT is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.


Freebayes is a high-performance, flexible, and open-source Bayesian genetic variant detector.

Genome Analysis Toolkit

GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects.

HH Suite

HHSuite The HH-suite 2.0.6 is an open-source software package for sensitive sequence searching based on the pairwise alignment of hidden Markov models (HMMs). It contains HHsearch and HHblits among other programs and utilities


Mira is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).



Picard-Tools comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.


PSIPRED is a protein secondary structure prediction tool based on position-specific scoring matrices.

“A two-stage neural network is used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and convenience of the approach used, the results are found to be superior to those produced by other methods, including the popular PHD methods…”


Qiime QIIME (pronounced “chime”) stands for Quantitative Insights Into Microbial Ecology.

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.


SamTools SAM stands for Sequence Alignment/Map SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.


Trinity a method for de novo assembly of full-length transcripts


USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases.


Velvet Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.

support/hpc/software/genomics.txt · Last modified: 2012/06/12 17:52 (external edit)