How to install Perl modules manually, using CPAN command, and other quick ways
...un - BioPerl wrappers: scriptslibbio-perl-perl - BioPerl core perl moduleslibbio-perl-run-perl - BioPerl wrappers: moduleslibbio-samtools-perl - Perl interface to SamTools library for DNA sequencinglib...3953 days ago
Converting a VCF into a FASTA given some reference !
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does th...ithub.com/gringer/bioinfscripts/blob/master/vcf2fq.pl https://github.com/lh3/samtools/blob/master/bcftools/vcfutils...2119 days ago
List of popular bioinformatics software/tools
In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.3948 days ago
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Structure of Binary files used for storing sequencing data-bam and sff
...t they occupy less space in memory with maximum information content. Link for those who looking for structure of Bam and sff file: Bam: http://samtools.sourceforge.net/SAMv1.pdf&nbs...3922 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...Research 22(5): 939–946. PubMedCentral Data formats, data management, and alignment software tools The Sequence Alignment/Map format and SAMtools. Li et al, Bioinformatics 25(...3782 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your system #Autho...$2 for you from $FASTAFILE -- MAKE SURE U HAVE ADDED CORRECT NAME" samtools faidx MergedContigs.fasta...2655 days ago
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"2357 days ago
Comment on "Setting up autoConTAMPR !"
......Setting up phyml (2:20120412-2) ...Setting up primer3 (2.3.6-1) ...Setting up probalign (1.4-3) ...Setting up probcons (1.12-9) ...Setting up samtools (0.1.19-1) ...Setting up sim4...1445 days ago
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