Comment on "SPAdes hybrid genome assembly"
...pass.2D.fastq -o SPAdes_hybrid & Use samtools to extract the top contig: head -n 1 SPAdes_hybrid/contigs.fasta samtools faidx SPAdes_hybrid/contigs.fasta samtools faidx SPAdes_hybrid...2313 days ago
2313 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...ads.fq reads.fq | gzip -1 > reads.paf.gz Then we can assemble miniasm -f reads.fq reads.paf.gz > reads.gfa Convert GFA to FASTA: awk '/^S/{print ">"$...2313 days ago
Comment on "Basic command-line to run BLAST"
...Avaga_protein/mouse.protein.faNew DB title: mouse.protein.faSequence type: ProteinKeep MBits: TMaximum file size: 1000000000BAdding sequences from FASTA; added 76216 sequences in 2.8...2383 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
.../Output options: -r, --ref STR Path to the reference sequence (fastq or fasta). -i, --index STR Path to the...es the format automatically from file extension. fastq - Loads FASTQ or FASTA files. fasta - Loads FASTQ or...2431 days ago
2937 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Rename the name of multi fasta sequesnces with awk awk '/^>/{print ">chromosome" ++i; next}{print}' < file.fasta3118 days ago
Comment on "Next generation sequencing in R or bioconductor environment"
...cal/reference/ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/http://hgdownload.cse.ucsc.ed...3759 days ago
Comment on "Bio++ : C Language libraries for your biological need"
Parse FASTA/FASTQ file with C http://lh3lh3.users.sourceforge.net/parsefastq.shtml4051 days ago