Comment on "Short-read assembly using Spades !"
...atic or FastQC. Running SPAdes: After quality control, the next step is to run SPAdes. This can be done through a command-line interface or a graphical user interface. The command for running SPAdes is usua...458 days ago
Comment on "Tools for Sequence translation !"
...n handle multiple sequences at once. EMBOSS Transeq: This is a command-line tool that can translate nucleoti...DNA or RNA sequences into protein sequences. SeqKit: This is a command-line tool that can perform several...463 days ago
Comment on "Basic command-line to run BLAST"
...m the search: Once the query sequence and parameters have been set, the BLAST search can be run. This can be done online using the NCBI BLAST website or locally using the command-line interface. Interpret the...466 days ago
Comment on "ncbi-datasets-cli -- Quickstart: command line tools !"
...TOOLS]$ curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets' % T...OLS]$ curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/dataformat...923 days ago
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Comment on "Sibelia: A comparative genomics tool"
...ectory for temporary files"). Above commands will run "Sibelia" on the fi...tions of the synteny block. It has two lines for each input sequence: 1. Header line -- FASTA header of the sequen...ahp for k=25, one can use the following command line: Sibelia -k run.s...1328 days ago
Comment on "List of gene ontology software and tools"
GeneSCF serves as command line tool for clustering list of genes based on functional annotation (Geneontology, KEGG, REACTOME and NCG). This tool requires gene list in the form of Entrez Gene IDs or Official gene symbols as a input. http://genescf.kandurilab.org/1535 days ago
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Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
... We need to download poRe from sourecforge and we are using version 0.16 Once downloaded, and back at the Linux command line: R CMD INSTALL poRe_0.16.t...2217 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...--verbose-sam INT Helpful debug comments can be placed in SAM output lines (at the end). Comments can be t...s increase/decrease verbosity level. 0 - verbose off 1 - server mode, command line will be omitted to obfuscate...2335 days ago