Results for "long reads"
Top-level pages
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 sel...sp;sequences. Thus the per-base error rate is similar to the raw input reads. Find the detail of the read...2369 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads to multiple genomes at once,...you want to determine whether reads are mouse or human, it does n..., either quantifying how many reads go to each reference, or spli...file for each of them. Paired reads will always be kept together....2354 days ago
- There are several ways you can convert fastq to fasta sequences....or many purposes. One such use is fastq-fasta conversion seqret -sequence reads.fastq -outseq reads.fasta awk can be used...
2344 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing fin...or.htm JVM Java Visual Mapping tool for NGS reads http://www.springer.com/cda/...gnments of huge-scale single-end and pair-end short reads http://omictools.com/mapview...2323 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 tools for NG...urrent directory ls -l — list items in current directory and show in long...2320 days ago
Awk for Bioinformatician and computational biologist
Awk is a programming language which allows easy manipulation of structured data and...n1/ {Actions} /pattern2/ {Actions}' file The working of Awk is as followsAwk reads the input files one line at a...2319 days ago
Some useful Bioinformatics links
...ULIP: TULIP - The Uncorrected Long read Itegration Pipeline http...apping of nanopore sequencing reads with GraphMap | Nature Commun...ols.html How To Filter Mapped Reads With Samtools https://www.bi...ithub.com/lh3/minimap2 SSPACE-LongRead: scaffolding bacterial dra...2281 days ago
Installing Bio::SCF perl module
Most Perl modules are written in Perl, some use XS (they are written in&...int... yeschecking size of int... 4checking for long... yeschecking size of long... 8checking for inline... in...squo;int’, but argument 3 has type ‘long...2257 days ago
- To remove all line ends (\n) from a Unix t...es into sets with mapped and unmapped reads: samtools view -F4 sample.ba...ut -d' ' -f1 < your_file To count reads in a all .fastq.gz files in y...fastq read length distribution: cat reads.fastq | awk '{if(NR%4==2) pri...
2256 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform ga...to fill the gap within paired reads" or "Toward almost closed gen...local re-assemblies using 454 reads. We used GAPresolution but it...of interest, and the set S of reads those contigs contain. Let C...ctor, and generate paired-end reads for this library; then try st...2204 days ago
