Jit
Enthusiast computational biologist with business dream !!!
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FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ...
By Shruti Paniwala 1506 days agogithub.com - FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1772 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...Reference-free prediction of rearrangement breakpoint reads
By Neel 2484 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...SuRankCo: supervised ranking of contigs in de novo assemblies
By Neel 2772 days agosourceforge.net - SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2290 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome...
By Jit 1789 days agogithub.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...Public Databases for Bioinformatics !
By Jit 1373 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 2583 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...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2574 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...String graph based genome assembly software and tools !
By Rahul Nayak 2563 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.
