Results for "concordant 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...2272 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...2234 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...
2209 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...2157 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...2174 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...2143 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...2088 days ago
Frequent parameters for bioinformatics tools !
...balign.task_options.min_accuracy: 70 Pbalign.task_options.no_split_subreads: false Genomic_consensus.task_opt...retools.task_options.other_filters: rq >= 0.7 Pbalign.task_options.concordant: false Genomic_consensu...1278 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...817 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...
575 days ago
