Jit
Enthusiast computational biologist with business dream !!!
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Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2747 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...ANItools web: a web tool for fast genome comparison within multiple bacterial strains
By Jit 2670 days agohttp://ani.mypathogen.cn/ - ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2136 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Abhi 1613 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)...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 571 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 3195 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
By Rahul Nayak 2123 days agogithub.com - LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2739 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...COSINE: non-seeding method for mapping long noisy sequences
By Jit 2689 days agogithub.com - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
By BioStar 2588 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly...
