2715 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...SnpEff Input: BAM Reference Genome: FASTA indexed with SAMtools...: VCF, BED Output: VCF (with new ANN field, also used in ANNOVAR...alf, CNV file -cnv Reference genome: -refgene (created in MATLAB,...nts in noncoding Annotations; New version released July 2015; Comm...2910 days ago
Tools for Searching Repeats And Palindromic Sequences
What are genomic interspersed repeats? I...960's scientists discovered that many genomes contain stretches of highly...been copied to another region of the genome.Interspersed RepeatsProcessed...which have been reintegrated into the genome with the assitance of a rever...2212 days ago
2870 days ago
Genome Assembly Tools and Software - PART1 !!
...alable and fully parallelized Genome Assembler There is a growing gap between the output of new generation massively parallel se...ontigs file, Bandage opens up new possibilities for analysing de n...er designed to assemble virus genomes that have no repeat sequence...2687 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates...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 genome by breaking into two sub-read...2523 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abunda...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 genome sequencing reads Software (P...2372 days ago
2352 days ago
Single Cell RNAseq data analysis tutorial !!
A major breakthrough (replaced microarrays) in the late 00’s and has been w...res and reveal cell-type-specific expression changes in type 2 diabetes http://genome.cshlp.org/content/early/2016/...2352 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (...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...or annotating fully sequenced genomes. PAGIT: Provides a toolkit...2332 days ago