Perl Special Vars Quick Reference
$_ The default or implicit variable. @_ Subroutine parameters. $a$b...Input / Output layer information. ${^UNICODE} Read-only Unicode settings. $...mplement scoped pragmas. ${^TAINT} Taint mode read-...2637 days ago
Quick next generation sequencing (NGS) terms definition
...ata set separately.concordant reads: a read pair is called...by definition, the discordant read pairs signal potential SVs. T...tion or deletion (indel).read depth: number of reads that ma...ome. Overall genome-wide read depth is also referred to as depth...2515 days ago
2482 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-seq...les of the RNA-seq paired-end reads Software (Java) https://gi...irectly from raw NGS sequence reads by counting unique k-me...ird-generation long and noisy reads (10 kbp) using a dimensional...classification of metagenomic reads...2364 days ago
2344 days ago
2344 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and output...s not have a consensus step. It simply concatenates pieces of read...2323 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads to multiple genomes at once,...ns an exact repeat somewhere, reads mapping to it will be mapped...you want to determine whether reads are mouse or human, it does..., either quantifying how many reads go to each reference, or spl...file for each of them. Paired reads...2308 days ago
List of visualization tools for genome alignments
...But sometime, we need publication ready figure of genomes. Following...Java Visual Mapping tool for NGS reads http://www.springer.com/cda...uencing technologies. Low- or high-depth read pileups and easy visual...ewer Visualization of short read alignment, identification of g...2277 days ago
Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals
The purpose of this cheat sheet is to introduce biologist and bioinformatician to the frequently used too...number between 0 and 7. 7 — full permissions 6 — read and write only 5 — read...2274 days ago