Abhimanyu Singh
A bioinformatics beginner
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Alien Genome !!!
By Jit 4255 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.
Tools to access the quality of your assembled genome !
Last updated 729 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...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 2383 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtLoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2892 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...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 2364 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 3145 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 3034 days agogithub.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...Converting a VCF into a FASTA given some reference !
By Jit 2940 days agoconverting a VCF file into a FASTA file given a reference sequenceLong read assembly workshop !
By Rahul Nayak 2864 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...SKESA: strategic k-mer extension for scrupulous assemblies
By Jit 2823 days agogithub.com - SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity,...
