Opera: An optimal genome scaffolding program
...hroughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y2363 days ago
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
...828 mouse TFs, respectively. They have been derived from 11,237 pubmed articles, which describe small-scale e...iently search for regulatory relationships from over 20 million pubmed articles, we used sentence-based text...2339 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
...nd additionally a file in the input format containing uncorrected reads. https://github.com/biointec/jabba/wiki https://almob.biomedcentral.com/articles/10.1186/s13015-016-0075-71994 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
...ty of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation. https://www.nature.com/articles/nmeth.45562320 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two conti...2249 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82210 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcrip...2202 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...bled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON. https://www.nature.com/articles/nmeth.44322199 days ago
2197 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
...ngle reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768987/2184 days ago