alan.cs.gsu.edu - caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one...
github.com - pyScaf orders contigs from genome assemblies utilising several types of information:
paired-end (PE) and/or mate-pair libraries (NGS-based mode)
long reads (NGS-based mode)
synteny to the genome of some related species (reference-based...
chibba.agtec.uga.edu - MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences...
www.ncbi.nlm.nih.gov - YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments....
github.com - MCE spawns a pool of workers and therefore does not fork a new process per each element of data. Instead, MCE follows a bank queuing model. Imagine the line being the data and bank-tellers the parallel workers. MCE enhances that model by adding the...
www.mgc.ac.cn - GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or...
github.com - Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive...
en.wikipedia.org - FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a...
Hi Bioinformatician and Computational Biologist, this is the comprehensive list of all (?) the bioinformatics and computational biology journals. Please update me if you know any other good journals related with our domains. Feel free to add...
