• BWA

  • Referenced in 50 articles [sw34374]
  • mapping low-divergent sequences against a large reference genome, such as the human genome ... such as long-read support and split alignment, but BWA-MEM, which is the latest...
  • TopHat

  • Referenced in 23 articles [sw17157]
  • TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines ... mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes...
  • BS Seeker

  • Referenced in 6 articles [sw23481]
  • single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated reads, where ... genome. It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes ... faster. When mapping to the human genome, BS Seeker generates alignments significantly faster than RMAP ... able to efficiently map reads to large mammalian genomes. The Python program is freely available...
  • STAR

  • Referenced in 14 articles [sw02515]
  • factor of >50 in mapping speed, aligning to the human genome 550 million ... server, while at the same time improving alignment sensitivity and precision. In addition to unbiased ... fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche...
  • GMAP

  • Referenced in 3 articles [sw17275]
  • GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Motivation: We introduce ... cDNA sequences to a genome. The program maps and aligns a single sequence with minimal ... minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice...
  • Circos

  • Referenced in 5 articles [sw27740]
  • routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses...
  • ECgene

  • Referenced in 4 articles [sw17328]
  • human genome map and fast algorithms for sequence alignment, genome-based EST clustering became ... Gene modeling by EST Clustering), which combines genome-based EST clustering and the transcript assembly ... exon–intron boundaries) in the genome map is utilized as the critical information...
  • SHRiMP

  • Referenced in 15 articles [sw17146]
  • methods to map short reads to a genome, even in the presence of a large ... based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space ... map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate...
  • BFAST

  • Referenced in 4 articles [sw20962]
  • freely available implementation, BFAST, which can align data produced by any of current sequencing platforms ... flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary ... mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align ... data needed to fully resequence a human genome, one billion reads, with high sensitivity...
  • BSMAP

  • Referenced in 5 articles [sw23515]
  • genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge ... alignments, and multiple CpG heterogeneous methylation. RESULTS: We developed an efficient bisulfite reads mapping algorithm ... address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast...
  • FASTX

  • Referenced in 2 articles [sw17090]
  • FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using ... specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many...
  • CloudBurst

  • Referenced in 6 articles [sw12025]
  • genotyping and personal genomics. It is modeled after the short read-mapping program RMAP ... reports either all alignments or the unambiguous best alignment for each read with any number ... core, while computing an identical set of alignments. Using a larger remote compute cloud with ... jobs involving mapping of millions of short reads to the human genome. Availability: CloudBurst...
  • BM-map

  • Referenced in 2 articles [sw10924]
  • mapped to a unique location, a significant proportion of reads align to multiple genomic locations ... these are called multireads. The ambiguity in mapping the multireads may lead to bias...
  • HISAT

  • Referenced in 5 articles [sw28860]
  • fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition ... global FM index that represents a whole genome, HISAT uses a large set of small ... collectively cover the whole genome (each index represents a genomic region ... human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective...
  • Maligner

  • Referenced in 1 article [sw34217]
  • aligner. Motivation: The Optical Mapping System discovers structural variants and potentiates sequence assembly of genomes ... publicly available tools for aligning optical mapping datasets. Results: Here we present software, named ‘Maligner ... restriction maps of sequence contigs to a reference. Maligner provides two modes of alignment ... large eukaryotic genomes, and a faster indexed based implementation for finding alignments with unmatched sites...
  • MicroRazerS

  • Referenced in 2 articles [sw34361]
  • MicroRazerS: rapid alignment of small RNA reads. Motivation: Deep sequencing has become the method ... cell. Mapping the sequenced reads onto their reference genome serves as the basis ... read aligners has established itself for the particular task of small RNA mapping. Results ... tool optimized for mapping small RNAs onto a reference genome. It is an order...
  • featureCounts

  • Referenced in 5 articles [sw17317]
  • sequence reads, which are usually aligned to a reference genome. In many applications ... downstream analysis is the number of reads mapping to each genomic feature, for example...
  • Xenomapper

  • Referenced in 1 article [sw29189]
  • that have been aligned to a primary genome and a secondary genome and binning reads ... pathogen interactions. Xenomapper is most effective with mapped reads that include...
  • CUSHAW

  • Referenced in 2 articles [sw34349]
  • parallel and efficient algorithms for NGS read alignment. Next generation sequencing (NGS) technologies have enabled ... have complicated the mapping of NGS reads onto the reference genome and have motivated ... development of various aligners for very short reads, typically less than 100 base pairs...
  • SNVMix

  • Referenced in 4 articles [sw29569]
  • short sequence reads that, once aligned to a reference genome sequence, can be interpreted ... inherent in genomically unstable tumor genomes. The second models nucleotide and mapping qualities ... base call and the read alignment. The third combines filtering out low-quality data ... genotyping arrays and a human breast cancer genome sequenced to >40× (haploid) coverage with ground...