2349 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
...r in unison on a wide variety of architectures. https://jgi.doe.gov/data-and-tools/meraculous/ https://arxiv.org/ftp/arxiv/papers/1703/1703.09852.pdf2341 days ago
ECTOOLS: Long Read Correction and other Correction tools
...correct long read data. More background information for the algorithm can be found:http://schatzlab.cshl.edu/presentations/2013-06-18.PBUserMeeting.pdf2326 days ago
2284 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
...arches with the same sensitivity as PSI-BLAST at over 400 times its speed. The MMseqs2 user guide is available as Github Wiki or as PDF file (Thanks to pan...2249 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
...ned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with...2186 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes locate...2180 days ago
EAGLER: a scaffolding tool for long reads.
...lowing operating systems: Mac OS X 10.11.1 Mac OS X 10.10.3 Ubuntu 14.04 LTS https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf2176 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...nerate 20 threads to run FinisherSC. python finisherSC.py -par 20 destinedFolder mummerPath Sometimes,...2099 days ago
S-plot2: creates an interactive, two-dimensional heatmap of sequences
...novel coding regions, and laterally transferred elements. http://www.putonti-lab.com/uploads/4/5/3/0/45307835/s-plot2_tutorial.pdf http://journals.sagepub.com/doi/pdf/10.1177/1176934318797354...2060 days ago