Results for "Reads"
Top-level pages
Awk for Bioinformatician and computational biologist
...en perform associated actions. The basic syntax is: awk '/pattern1/ {Actions} /pattern2/ {Actions}' file The working of Awk is as followsAwk reads the input files one line at a...2268 days ago
Some useful Bioinformatics links
...deletions, from raw set(s) of reads. https://github.com/GATB/Dis...nome from nanopore sequencing reads | Scientific Reports https:/...apping of nanopore sequencing reads with GraphMap | Nature Commun...ols.html How To Filter Mapped Reads With Samtools https://www.bi...2230 days ago
- ...t bam files into sets with mapped and unmapped reads: samtools view -F4 sample.ba...aders: cut -d' ' -f1 < your_file To count reads in a all .fastq.gz files in y...To get fastq read length distribution: cat reads.fastq | awk '{if(NR%4==2) pri...
2206 days ago
Gap filling or Contigs extensions tools !
...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...2154 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ &&am...2171 days ago
LINKS scaffolder bloomfilter setting !
...TA format, required) -s file-of-filenames, full path to long sequence reads or MPET pairs [see below] (Multi-FASTA/fastq format, required) -m MPET reads (default -m 1 = yes, default...2140 days ago
List of non-commercial NGS genotype-calling software
...SFS http://128.32.118.212/thorfinn/realSFS/ Single-sample Aligned reads Software for SNP and genotype...mation Samtools http://samtools.sourceforge.net/ Multi-sample Aligned reads Package for manipulation of N...2085 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. You ca...we used above: illumina_R1.fastq.gz: the Illumina forward reads illumina_R2.fastq.gz: the Illumina reverse reads Assemble Run Spades: s...814 days ago
- ...tly, many of the popular short read simulators are designed to simulate reads mimicking many Illumina, 454...ntly, many of the popular long read simulators are designed to simulate reads mimicking the two main TGS te...
572 days ago
Bioinformatics tools for genome assembly !
...ruijn graph-based assembler designed for short reads, widely used for assembling l...SMARTdenovo: An assembler designed for long reads, particularly suited for PacB...rc: An assembler designed to handle noisy long reads from Nanopore sequencing....275 days ago
