Software packages for next gen sequence analysis
Integrated solutions * CLCbio Genomics Workbench - de novo and ref...uences produced on a Illumina Genome Analyzer. A suite created by...f Nucleotide Databases. Whole genome alignments to a reference gen...na reads to a FASTA reference genome. By Andrew D. Smith and Zheny...om the Canada's Michael Smith Genom...3240 days ago
Comprehensive list of visualization tools for biological pathways
The study of biological pathways is a key to understand the different processes inside a cell: proteins exer....kazusa.or.jp/ KEGG Atlas Interactive Kyoto Encyclopedia of Genes and Genomes pathways http://www.genom...2285 days ago
2712 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
Commercial tools Strand NGS offers many different tools incl...d text files Supports custom genome builds and annotation databas...gzipped or not; no reference genome required; read pairs can be g...SnpEff Input: BAM Reference Genome: FASTA indexed with SAMtools...alf, CNV file -cnv Reference genom...2906 days ago
Tools for Searching Repeats And Palindromic Sequences
What are genomic interspersed repeats? In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive D...have been copied to another region of the genome.Interspersed RepeatsProcessed...nes which have been reintegrated into the genom...2209 days ago
2867 days ago
Genome Assembly Tools and Software - PART1 !!
...reported for the assembly of genomes while the others are designed aiming at handling complex genomes. TriMetAss 1.2 – Th...alable and fully parallelized Genome Assembler There is a growi...er designed to assemble virus genomes that have no repeat sequence...Phusion 2.1c – Assembly Genom...2683 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates paired-end reads from both ends...d concordant if they can be mapped to the reference genome as “expected”: (a...bsp;a read that can only be mapped to the reference genom...2520 days ago
Awesome perl frameworks, libraries and software - PART 1
A curated list of awesome Perl frameworks, l...rap and Font-Awesome. fletcher/SimplenoteSync - perl routine to sync folder of text files with your notes on Simplenote tobert/perl-ss...nphilp/Perl-gtk3-Tutorial - Some notes on using Gtk3 with Perl keso...2487 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-seq d...https://github.com/bioinfo-ut/GenomeTester4/ Phy-Mer Reference-i...SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from ra...., ONT or PacBio reads, draft genomes) Software (Perl) https://g...ol for MLST directly from the genom...2369 days ago