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• Best way to remove contaminants to get nuclear genome
  I have plant genomic reads (WGS method) through hiseq 2000 with paired-end reads (read1.fastq, r...
• What genome assembler to choose for an unpaired FASTQ data derived from a Birch chloroplast?
  What genome assembler to choose for an unpaired FASTQ data derived from a Birch chloroplast? And...
• Downloading rice chloroplast genome
  Hi, From where to download the fully sequenced chloroplast genome of rice (oryza sativa japonica...
• How to annotate chloroplast genome
  I mapped sequencing reads to a published chloroplast genome. A annotation file is available for t...
• Removing contaminations from PacBio reads
  Hi I have PacBio RS II and Sequal reads. I am looking for a tool which removes common contaminati...
• How can I use BLAST to extract chloroplast sequences from DNA reads?
  I'm trying to extract the chloroplast sequences from my reads, as Whole Genome Sequencing was use...
• Chloroplast 16S sequences - any fun to be had?
  I am working with some 16S sequences (V4 region) from soils. I am looking at bacterial diversity ...
• Filter Fastq file by seq
  Dear All: Does anyone know an efficient tool or script that removes certain reads with from Fastq...
• Remove reads from fastq file
  Hi, Could someone please help me with removing reads from a fastq file from a specific genomi...
• Filtering BAM file to extract PE reads that mapped as proper pairs, including PE reads that did not map, but their mate did
  Hi! I'm working on the assembly of a chloroplast genome. I have a bam file and I wanted to: 1....
• removing adapters based on IDs not sequence
  I am using cutadapt to remove the adapters from fastq file. in the paper I got the data from it m...
• How to remove reads from fastq flle that match to a set of reads in my fasta file?
  I have a fastq file that seems to be contaminated by some sequences contaminating my reagents dur...
• Removing PCR duplicates - fastq or BAM?
  Wondering about pros/cons of removing duplicates from the raw fastq files vs the raw BAM alignmen...
• Removing Reads Which Have Adapter Sequences
  Hi I would like to remove all those reads from my fastq file which has adapter sequence in it. ...
• Remove Singletons From Trimmed Fastq Files
  How are you removing singletons from whole exome data fastq files from which the adapter sequence...
• How to set FASTQ trimming parameters before de novo assembly of the birch chloroplast genome?
  How to set FASTQ trimming parameters before de novo assembly of the birch chloroplast genome? Ho...
• removing sequencing gaps
  Could anyone tell me how to remove sequencing gaps from a *.sam file?  I use bwa to map the refe...
• How To Detect Contamination Or Sample Preparation Artifacts In Sequencing Results
  Hi, Is there any tool (apart from fastQC) to detect all primers/adapters(contaminants basically)...
• Newbler seems stop
  I use Newbler to assembly chloroplast genome, with 2 fastq files. It's almost 1.2 million pair re...
• removal of spesific read from fastq file
  Hellow, Can someone kindly let me know that how to remove a specific read from paired end fastq f...
• filter_fasta.py not removing sequences from fastq based on read IDs
  I'm attempting to use [filter_fasta.py][1] in macqiime to remove sequences from a fastq based on ...
• Removal of Prevotella Copri sequence from a FASTQ/A file
  Hi All, We have fastq files from a gut microbiome projects. I used 16S metagenomic kit from Ion ...
• Primer sequences in fastq files from 16s rRNA experiment
  Hi there, I am working on the analysis of 16s RNA datasets using mothur toolkit. In the fastq f...