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mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2396 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Manisha Mishra 1964 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 256 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...Tigers genome sequenced
By Rahul Agarwal 4644 days agoOnly 4.4 percent DNA difference between Tiger and house catsOpera: An optimal genome scaffolding program
By Jit 3113 days agosourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 3111 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...String graph based genome assembly software and tools !
By Rahul Nayak 3090 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.AliTV—interactive visualization of whole genome comparisons
By Jit 3069 days agogithub.com - AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are...Carefully opt for human reference genome
By biogeek 2300 days agolh3.github.io - Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2948 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...
