Anjana
Bioinformatics enthusiast
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My commonly used commands in Bioinformatics
Last updated 2784 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...Arvados
By Martin Jones 4189 days agohttps://arvados.org/ - Arvados is a free and open source bioinformatics platform for genomic and biomedical data. User can Store | Organize | Compute | Share the data for free.Referee: Genome assembly quality scores
By Jit 2683 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 2419 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 2233 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1893 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...JRF/SRF at Jawaharlal Nehru Institute ofAdvanced Studies (JNIAS), Hyderabad
Applications for Academic Projects in Biotechnology, Bioinformatics, Environmental Sciences and Computer Science & Engineering About JNIAS Jawaharlal Nehru Institute of Advanced Studies (JNIAS), Hyderabad has been established by Dr. D....COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3016 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...Google Genomics
By Reshma Khatun 4162 days agocloud.google.com - Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure. Store alignments and variant calls for one genome or a million. Process...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2871 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...
