MMseqs2.0: ultra fast and sensitive protein search and clustering suite
...in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can ru...2264 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
...s in the output scaffolding to contigs in the reference scaffolding in the sense of the number of correct links. https://github.com/mandricigor/repeat-aware2265 days ago
Many-to-many pairwise alignments of two sequence sets
...bal sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programmi...2176 days ago
Carefully opt for human reference genome
...sed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the following: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/...1567 days ago
SciLifeLab tutorial for bioinformatics analysis !
...to Bioinformatics Using NGS Data 2015 February - Uppsala 2015 May - Gothenburg2015 September - Uppsa...ember - Uppsala2016 November - Umeå2017 January - Uppsala2017 May - Gothenburg2017 September - Lund2...2239 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Usi...2238 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...ctural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final ali...2231 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps be...2221 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
...s its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved prese...2218 days ago
Metassembler: merging and optimizing de novo genome assemblies
...individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find t...ary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple ass...2218 days ago