:: DESCRIPTION
Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.
::DEVELOPER
The Center for Computational Biology at Johns Hopkins University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Diamund is a new, efficient algorithm for variant detection that compares DNA sequences directly to one another, without aligning them to the reference genome.
::DEVELOPER
The Center for Computational Biology at Johns Hopkins University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Mutat. 2014 Mar;35(3):283-8. doi: 10.1002/humu.22503.
DIAMUND: direct comparison of genomes to detect mutations.
Salzberg SL, Pertea M, Fahrner JA, Sobreira N.
:: DESCRIPTION
HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads.
HISAT2 is a successor to both HISAT and TopHat2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
::DEVELOPER
The Center for Computational Biology at Johns Hopkins University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
HISAT: a fast spliced aligner with low memory requirements.
Kim D, Langmead B, Salzberg SL.
Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317.
:: DESCRIPTION
Bowtie is an ultrafast, memory-efficient short read aligner. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds.
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
::DEVELOPER
the Center for Bioinformatics and Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Langmead B, Trapnell C, Pop M, Salzberg SL.|
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biology 10:R25.
:: DESCRIPTION
Dmatch is a method that leverages an external expression atlas of human primary cells and kernel density matching to align multiple scRNA-seq experiments for downstream biological analysis.
::DEVELOPER
Chen Group at U Chicago
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen M, Zhan Q, Mu Z, Wang L, Zheng Z, Miao J, Zhu P, Li YI.
Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.
Genome Res. 2021 Apr;31(4):698-712. doi: 10.1101/gr.261115.120. Epub 2021 Mar 19. PMID: 33741686; PMCID: PMC8015859.
:: DESCRIPTION
PEANUT is a read mapper for DNA or RNA sequence reads. Read mapping is the process of aligning biological DNA or RNA sequencing reads to a known reference genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Köster J, Rahmann S (2014).
Massively parallel read mapping on GPUs with the q-group index and PEANUT.
PeerJ 2:e606 http://dx.doi.org/10.7717/peerj.606
:: DESCRIPTION
Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rausch T, Hsi-Yang Fritz M, Korbel JO, Benes V.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.
Bioinformatics. 2019 Jul 15;35(14):2489-2491. doi: 10.1093/bioinformatics/bty1007. PMID: 30520945; PMCID: PMC6612896.
:: DESCRIPTION
Wasabi is a tool for visualisation and manipulation of rich MSAs and a graphical interface to command-line programs.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.
Veidenberg A, Medlar A, Löytynoja A.
Mol Biol Evol. 2016 Apr;33(4):1126-30. doi: 10.1093/molbev/msv333.
:: DESCRIPTION
Many important principles underlying how protein molecular machines work lie beyond the pale of direct experimental observation. CHAIN (Contrast Hierarchical Alignment and Interaction Network ) analysis is a statistical solution to this problem that follows Mendel’s example: Just as Mendel inferred principles underlying genetic mechanisms from observed patterns of inherited traits, CHAIN analysis seeks to infer principles underlying molecular mechanisms from observed patterns in protein sequences—the cell’s own language for encoding those mechanisms.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Trends Biochem Sci. 2007 Nov;32(11):487-93. Epub 2007 Oct 24.
The CHAIN program: forging evolutionary links to underlying mechanisms.
Neuwald AF
:: DESCRIPTION
GISMO is a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA)
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
Neuwald AF, Altschul SF.
PLoS Comput Biol. 2016 May 18;12(5):e1004936. doi: 10.1371/journal.pcbi.1004936.
