Results for "Genome"
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GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules. I...Tags: GenomeTools, versatile, open, source, genome, analysis, software
817 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. https://academic.oup.com/nar/article/47/11/e63/537...Tags: MitoZ, toolkit, animal, mitochondrial, genome, assembly, annotation, visualization
880 days ago
ncbi-datasets-cli -- Quickstart: command line tools !
Install and use the NCBI Datasets command line tools The NCBI Datasets datasets command line tools are datasets and dataformat . Use datasets to download biological sequence data across all domains of life from NCBI. Use dataformat to convert metadata fr...Tags: ncbi-datasets-cli, database, download, ncbi, genome, genes, datasets
874 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (p...Tags: assembly, pipeline, genome, illumina
871 days ago
Refseq viraal genome sequences !
List of all viruses on NCBI https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/Tags: nvbi, viruses, genome, data, ftp
870 days ago
- With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Genome Atlas Project has sequenced over 30 different cancers with sample size of each cancer type being over 200. Resulting data consisting of somati...
Tags: maftools, maf, format, snp, variant, genome, mutation
864 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs from other species identified by PLAR. Available&nb...Tags: lncRNA, data, human, genome, plar
843 days ago
- compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@uss...
Tags: bwa, mapping, genome, vcf, align, genome
831 days ago
CrossMap: program for genome coordinates conversion between different assemblies
CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF,&nb...Tags: CrossMap, program, genome, coordinates, conversion, different, assemblies
824 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina forward reads illumina_R2.fastq.gz: the Illumina reve...Tags: spades, assembly, short, reads, genome, tools
819 days ago
