RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
...across the genomes. For more information, please see the academic paper published online (http://www.sciencedirect.com/science/article/pii/S071734581630001X).2217 days ago
2215 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye, J., Rhie,...2214 days ago
mScaffolder: A comparative genome scaffolding tool
...gnments to the reference genome. Please send your questions and comments to mchakrab@uci.edu. Citation https://www.nature.com/articles/s41588-017-0010-y2214 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...a > aln.sam # spliced long reads ./minimap2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf...2209 days ago
CGView - Circular Genome Viewer
...erver.gview.ca/ http://stothard.afns.ualberta.ca/cgview_server/ Paper https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx081/40374582209 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
...which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Il...2200 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast,...2200 days ago
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
...GaTOR 3, increases modularity, improves scaleability, extends input/output options, brings new network views and analysis algorithms. http://142.150.188.236/navigatorwp/2196 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...AT. For more extensive documentation please visit: https://kat.readthedocs.org/en/latest/ https://academic.oup.com/bioinformatics/article/33/4/574/26643392044 days ago