2270 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ fo...2250 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/s12864-017-3927-82211 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...ntact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a use...2197 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...aff, leverages coincidences between the content of different pools as a source of contiguity information for...in vivo cloning steps. Further information about fragScaff, including source code, is available at:https:/...2197 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
...any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...2197 days ago
2197 days ago
LAMSA: fast split read alignment with long approximate matches
...ly faster than the state-of-the-art long read aligners; mean-while, it also has good ability to handle various categories of SVs. LAMSA is open source and free for non-commercial u...2196 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
...ructural feature. The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts for analysis are included. The source code is available at http://g...2189 days ago
WhatsHap: fast and accurate read-based phasing
...s multi-sample VCFs. It produces standard-compliant VCF output by default If desired, get output that is compatible with ReadBackedPhasing Open Source (MIT license)...2183 days ago