BOL

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...

NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...

gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...

Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason. Given a fastq file in Illumina 1.8+/Sanger format, calculate the mean (rounded) score for each position and...

Understanding PairedEnd(PE) mapping https://davetang.org/muse/2014/07/24/getting-started-paired-end-reads/ #PE #Paired #End #PairedEnd #Mapping #Map #Learn

➜ bin git:(master) ✗ ./canu usage: canu [-version] [-citation] \ [-correct | -trim | -assemble | -trim-assemble] \ [-s <assembly-specifications-file>] \ -p <assembly-prefix> \ -d <assembly-directory> \...

du -sh * | sort | grep "G" #List size of all the directory #Size #List #Directory #Linux

# Index the draft genome bwa index draft.fa # Align the basecalled reads to the draft sequence bwa mem -x ont2d -t 8 draft.fa reads.fa | samtools sort -o reads.sorted.bam -T reads.tmp - samtools index reads.sorted.bam python...

#Remove #smartbell from #pacbio #removesmartbell.sh https://github.com/BioInfoTools/BBMap/blob/master/sh/removesmartbell.sh

Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...