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Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1682 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 1599 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...Alien Genome !!!
By Jit 4313 days agoGenome sequencing, analysis and expression of Alien genome. Note: This image/cartoon is create only for fun. It has nothing to do with any scientific findings.Jvarkit : Java utilities for Bioinformatics
By Jit 3040 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics
Tools to access the quality of your assembled genome !
Last updated 786 days ago by LEGEFASTA VALIDATOR + SEQKIT RMDUP: FASTA validation GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation ASSEMBLATHON STATS: Assembly statistics GENOMETOOLS GT STAT: Annotation statistics NCBI FCS ADAPTOR: Adaptor contamination pass/fail NCBI...LSC :a long read error correction tool
By Jit 2985 days agowww.healthcare.uiowa.edu - Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2938 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...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 3056 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 2441 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 2108 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...
