Results for "discordant reads"
Top-level pages
Awk for Bioinformatician and computational biologist
Awk is a programming language which allows easy manipulation of structured data and is m.../ {Actions} /pattern2/ {Actions}' file The working of Awk is as followsAwk reads the input files one line at a...2280 days ago
Some useful Bioinformatics links
Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxford Aca...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...2241 days ago
- To remove all line ends (\n) from a Unix text fi...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...
2217 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de...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...2165 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...2182 days ago
LINKS scaffolder bloomfilter setting !
➜ bin git:(master) ✗ ls -l total 68 drwxrwxr-x 3 urbe urbe...-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...2151 days ago
List of non-commercial NGS genotype-calling software
Meaningful analysis of next-generation sequencing (NGS) data,...2.118.212/thorfinn/realSFS/ Single-sample Aligned reads Software for SNP and genotype...://samtools.sourceforge.net/ Multi-sample Aligned reads Package for manipulation of N...2096 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...825 days ago
- Short Read Simulators With the popularity of next-generation...lar short read simulators are designed to simulate reads mimicking many Illumina, 454...ular long read simulators are designed to simulate reads mimicking the two main TGS te...
583 days ago
Bioinformatics tools for genome assembly !
There are numerous genome assembly tools availab...ph-based assembler designed for short reads, widely used for assembling l...enovo: An assembler designed for long reads, particularly suited for PacB...sembler designed to handle noisy long reads from Nanopore sequencing....286 days ago
