2283 days ago
ARCS: scaffolding genome drafts with linked reads
...ium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.2264 days ago
GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2249 days ago
2220 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
...thods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequ...2201 days ago
CrossMap: a program for convenient conversion of genome coordinates
...Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome. We do...2178 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...rmation from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative inf...e TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from...2174 days ago
BEAP: Blast Extension and Assembly Program
...to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or in...e disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known...2167 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbia...2167 days ago
Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global seque...um alignment (including gaps) of two sequences along their entire length. Th...ng and extending gaps in the aligned sequences. The substitution matrix and...2159 days ago