Seal: SEquence ALignment evaluation suite
...reference genome from one or more FASTA files. Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability ra...2372 days ago
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://gen...2337 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
...issues which hinders from an adequate scaffolding evaluation are genome repeats. The previous standard for e...(Hunt et al., Genome Biology, 2014) did not take into account repeats. In this evaluation framewor...2295 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...ruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repeat classification and analysis s...2251 days ago
HALC: High throughput algorithm for long read error correction
...uirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach)...2216 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, th...2143 days ago
QUAST-LG: Versatile genome assembly evaluation
...blies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage reg...2077 days ago
Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
...-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable ele...1859 days ago
RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and re...1641 days ago
1631 days ago