Results for "Fasta"
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Comment on "Short-read assembly using Spades !"
...output: Once SPAdes has finished running, check the output directory for the assembled contigs. The contigs will be saved in a file named contigs.fasta. You can view the contigs usi...413 days ago
Comment on "Basic command-line to run BLAST"
...nd tblastx. Choose the program that is appropriate for your query and database. Prepare the query sequence: The query sequence should be in a FASTA format and can be entered dir...415 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...p.paf.gz > miniasm.gfa awk ’/^S/{print “>”$2”\n”$3}’ miniasm.gfa > miniasm.fasta assembly-stats ./miniasm.fasta dnadiff -p dnadiff ~/course_...788 days ago
Comment on "Command line to create blast uniref database !"
wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz gunzip -v uniref90.fasta.gz makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90.fasta938 days ago
- ...ble command line options. $ ./fastANI -h One to One. Co...single reference genome: $ ./fastANI -q [QUERY_GENOME] -r [REFER...are the query genome assemblies in fasta or multi-fasta format. One...ltiple reference genomes: $ ./fastANI --ql [QUERY_LIST] --rl [REF...
1094 days ago
- DeepConflation based CNN model is used to generate alignment of fasta file . Model try to match a query string in a referance genome to provide location of match. https://github.com/gguptaiitd/DeepConflation
1138 days ago
Comment on "URMAP, an ultra-fast read mapper"
...ommand Maps unpaired reads to a reference genome. The reference genome is stored as a UFI file created by the make_ufi command. The original FASTA file for the reference is not...1276 days ago
Comment on "Sibelia: A comparative genomics tool"
...-s loose Helicobacter_pylori.fasta Important note -- "Sibelia...elia" on "Helicobacter_pylori.fasta" with "fine" parameters set,...loose -a Helicobacter_pylori.fasta Synteny blocks are visuali...equence: 1. Header line -- FASTA header of the sequence (start...1277 days ago
Comment on "Mugsy: multiple whole genome alignment tool"
... mugsy --directory /data/output --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta This exampl...the output files (eg. genome1 from genome1.fsa). Header lines in the FASTA files should not contain ':'...1278 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
... canonical hashes for both sequence 1 and 2, as well as 8 threads. Finally, clean up you working directory by removing the combined fasta file, and re-zipping any unzi...1329 days ago
