BBTools for bioinformatician !
...,nextera.fa.gz" and get them all (this will increase the amount of overtrimming, though it should still be ne...BBDuk.sh BBDuk can operate in one of 4 kmer-matching modes:Right-trimming (ktrim=r), left-trimming (ktr...2263 days ago
CANU genome assembly parameters !
...ter correction, trim and split based on consensus evidence. *.trimmedReads.fastq : file containing the sequences after correction and final trimming *.layout : file contain...1937 days ago
3226 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_...2934 days ago
Genome Assembly Tools and Software - PART2 !!
...between contigs. Lucy 2.20 – DNA Sequence Quality & Vector TrimmingLucy has been used for se...rior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of...2678 days ago
2706 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...data (.fastq, BAM, SAM), microarrays (Affymetrix, Illumina) and text files Supports custom genome builds and annotation databases Performs base trimming, alignment, quantification, q...2901 days ago
3911 days ago
Installing Porechop on Ubuntu !
...on] Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and split...p extend (default: 3,-6,-5,-2) End adapter settings: Control the trimming of adapters from read ends...2098 days ago
2067 days ago
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
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 reads, bad reads and the QC results of each fastq fi...Tags: Automatic, Filtering, Trimming, Error, Removing, Quality, Control, fastq, data
2357 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it suppo...Tags: Automatic, Filtering, Trimming, Error, Removing, Quality, Control, fastq, data
2129 days ago
Comment on "nanofilt: Filtering and trimming of long read sequencing data"
Nanofilt steps https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/2032 days ago
Comment on "Installing Porechop on Ubuntu !"
...(forward) 75.0 76.9 Barcode 93 (forward) 76.0 80.0 Barcode 94 (forward) 75.0 76.0 Barcode 95 (forward) 80.0 80.8 Barcode 96 (forward) 79.2 76.0 Trimming adapters from read ends SQK-N...2098 days ago