EAGLER: a scaffolding tool for long reads.
EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the...2214 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) r...ng large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT tak...2238 days ago
LAMSA: fast split read alignment with long approximate matches
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and goo...It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes tak...2234 days ago
TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as pr...additional components and/or implementations are likely to follow. Tulipseed tak...2234 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The fol...erent NGS reads. profile: Creates a K-mer coverage plot for a single sequence. Tak...2033 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of g...2066 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however...ere are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee tak...2060 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or mor...op computer using only the read sequences and a transcriptome index that itself tak...1997 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a sta...1982 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanop...arge mammalian-scale assemblies. The package represents a complete pipeline: it tak...1911 days ago