BBTools for bioinformatician !
...in=assembly1.fa,assembly2.fa out=merged.fa That will absorb exact duplicates and containments. You can use...a read came from; in other words, it can't remove only reads that are duplicates across multiple files but lea...2285 days ago
2908 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...a reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written t...1759 days ago
Genome of Rainbow Trout Sequenced
...here are fewer duplicated genes still present. Most of the duplicated genes get lost or modified so much that they are no longer recognizable as duplicates over time. In the trout and s...3677 days ago
Samtools commands for bioinformatician !
...total+=1}END{print (total/c)*100}' ### flagstat # output file has two columns: QC-passed reads and QC-failed reads # and rows: total reads, duplicates, mapped. samtools flagstat s...1617 days ago
Bash script to alignment of short reads against reference genome !
...w.bam --- sort the BAM file, writing it to .sorted.bam. #marking PCR duplicates: sambamba markdup SRR1770413....SRR1770413.bam --- this marks reads which appear to be redundant PCR duplicates based on their read mapping p...1573 days ago
Comment on "R and Bioconductor Tutorial"
NGS with R ShortRead – Quality assesment of the reads, finding duplicates, trimming, string pattern searches [1] Biostrings – Reading sequences in R [2] BSGenomes &ndas...3684 days ago