2742 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...2937 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...ve been copied to another region of the genome.Interspersed RepeatsProcessed...s which have been reintegrated into the genome with t...2239 days ago
2897 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...2714 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates paired-end reads from both end...concordant if they can be mapped to the reference genome as “expected”: (a...p;a read that can only be mapped to the reference genome by bre...2550 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...2399 days ago
2379 days ago
Single Cell RNAseq data analysis tutorial !!
A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the...and reveal cell-type-specific expression changes in type 2 diabetes http://genome.cshlp....2379 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsyst...ation (if you have only a few genomes to annotate). Prokka &...y useful if you have loads of genomes or need to annotate a pangen..., as well as other functional genome units such as structural RNAs...2360 days ago