BOL

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...

Overlap Layout Consensus assembly http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf #OLC #Assembly

Comparison of the two major classes of #assembly algorithms: overlap–layout–consensus and de-bruijn-graph https://academic.oup.com/bfg/article/11/1/25/191455

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...

hybrid assembly pipeline for bacterial genomes with Unicycler: https://github.com/rrwick/Unicycler #Unicycler #Hybrid #Bacteria

Sort a file with column 2: sort -g -k 2,2 allPacbio.fa.fai > sorted.fai #sort #file #column

Get the reads in fastq file: awk '{s++}END{print s/4}' file.fastq #reads #count #ngs #fastq

Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read...

Try BBMAP filterbyname.sh in=file.fa out=filtered.fa names=contig1,contig2

>AAAAGTCGTGC >BBBAGTGCGGGTG Remove AAA and keep only BBB

De Bruijn graph Tutorial http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_dbg.pdf #Assembly #Tutorial #DeBruijn

One interesting approach that gave good results in other genome projects - do several cycles of SSPACE / GapCloser/ REAPR (to detect misassemblies and break them). Usually after 4-6 cycles this converge on an optimal assembly and the statistics...

kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...

I am working on genome assembly, but wordering the optimised method to achieve the best result. Your comments and suggestions are welcome. 

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...

Understanding alignment https://www.cs.umd.edu/class/fall2011/cmsc858s/Alignment.pdf #Alignment #Learn