Files must be in fastq format and can be gzipped.
tabix -h ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 17:1471000-1472000 | perl vcf-subset -c HG00098 | bgzip -c /tmp/HG00098.20100804.genotypes.vcf.gz The filtered_fastq files contain reads passing the DCC fastq QC process and have been put on the ftp site. The input to the DCC QC pipeline are all fastq files retrieved from ERA, including reads generated by all three pilots and the main… Fastq format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. The 1000 Genomes project is really oriented to producing.vcf files; the file "ceu20.vcf" contains all the latest genotypes from this trio based on abundant data from the project..bam files containing a subset of mapped human whole exome… Test of compression ratio and speed of popular generic compression algorithms - DavidStreid/fastq-compression The emerging next-generation sequencing (NGS) is bringing, besides the natural huge amounts of data, an avalanche of new specialized tools (for analysis, compression, alignment, among others) and large public and private network… Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
A project to test my `rnaseq_workflow` repository. Includes rnaseq_workflow as a subtree - russHyde/test_rnaseq_workflow Download the RepeatMasker out files from the UCSC Genome Browser. For GRCh37 (hg19), this file is at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromOut.tar.gz :microscope: Assemble large genomes using short reads - staceb/abyss Contribute to orcnyilmaz/Calculating-K-mers development by creating an account on GitHub. cd [top_dir]/kmer_count readlink -f [top_dir]/trimmed/*.fastq > files.lst # We want all files kmc \ -k19 \ # Kmer size (19) -fq \ # Files are in fastq -m100 \ # Memory to use (100G) -t16 \ # No.
While the conversion of Fasta/Fastq files to Fasta+ files may take a few minutes, it needs to be done only once for data storage, and the resulting saving in storage space, internet traffic, and computation time in downstream data analysis… lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data. SNP calling, annotation and gene/transcripts expression quantification wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00313/sequence_read/ERR016234_1.filt.fastq.gz wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00313/sequence_read/ERR016234_2.filt.fastq.gz hdfs dfs -mkdir /data/input… MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes - linzhi2013/MitoZ
samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.Illumina.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455 These files contain the FTP url for each sequence fastq file, as well as other metadata information about the sequencing run and file. NanoSwe: Analysing nanopore (PromethION) data of Swedish genomes - Nazeeefa/NanoSwe Creation of Mutant Genomes/Reads. Contribute to lowandrew/MutantCreator development by creating an account on GitHub. A tool to identify ethnicity given a vcf file and to generate ethnic population-specific reference genomes - alexanderhsieh/ethref Automated human exome/genome variants detection from Fastq files - WGLab/SeqMule
Download and decompress 1000 Genomes phase 3 data . the log files and move them to the log directory here after each analysis step. refdir=~/reference.