Many-to-many pairwise alignments of two sequence sets
...m all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needlema...method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. A scor...2146 days ago
LAMSA: fast split read alignment with long approximate matches
...relatively long fragments and co-linearly align them to solve the small variations or sequencing errors, and mitigate the effect of repeats. The alignments of the fragments are then use...2181 days ago
TULIP - The Uncorrected Long read Integration Pipeline
.... These are very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse...2181 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format...2172 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align agai...2171 days ago
mScaffolder: A comparative genome scaffolding tool
...ence. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Plea...2150 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...me assemblies. Its underlying procedure follows a similar workflow as described by Goris et al. 2007. However, it avoids expensive sequence alignments and uses Mashmap as...2122 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analys...2097 days ago
SimLoRD: A read simulator for third generation sequencing reads
...s depend on fragment length. Provided subread error probabilities are modified according to number of passes Outputs reads in FASTQ format and alignments in SAM format...2082 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
...olutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamical...2080 days ago