Jit
Enthusiast computational biologist with business dream !!!
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nanofilt: Filtering and trimming of long read sequencing data
By Jit 2965 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...Nieduszynski Group
Complete, accurate replication of the genome is essential for life. All chromosomes in eukaryotic cells must be duplicated and then segregated to daughter cells to ensure genetic integrity and produce the large number of cells that make up a...orthodotter: Synteny plots (oxford grid)
By Jit 3320 days agogithub.com - orthodotter -h -------------------------------------------------------------------------------- orthodotter - Plot orthologous genes on an oxford grid. -f <file> : input file, containing orthologous genes, default is stdin...LoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 3441 days agowww.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
By Jit 3171 days agogithub.com - proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2927 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...pbmm2:A minimap2 frontend for PacBio native data formats
By BioStar 2397 days agogithub.com - pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3467 days agoStructural variation caller tools using long readsrHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2910 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...LAST
By Bulbul 3553 days agohttp://last.cbrc.jp/ - LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA...
