Assenbly and mate pair processing ?

Hello,

I'm in charge of a genome assembly. I have PE data and mate pair.

I usually perform a QC step with trimmomatic for my PE data. However, I've never deal with mate pair ... does it has to be trimmed too ? which software can you recommend ?

mate pair

• 1,613 views • link

written 10.2 years ago by Picasa

See if this helps with mate pair question: http://seqanswers.com/forums/showthread.php?t=28951

These two things may be useful as well: http://www.illumina.com/documents/products/technotes/technote_nextera_matepair_data_processing.pdf and NxTrim.

• 0 views • link

written 10.2 years ago by GenoMax

0 answers

No answers yet.

More posts like this

Metatranscriptome pipeline: taxonomy and functional recover
written 2.0 years ago by l.gallucci •

Hi all, I'm actually trying to build a pipeline for microbial transcriptome data (Illumina 2x150 bp). Basically up to now my work was based on …
FastQC Kmer Content
written 6.4 years ago by KSS •

Hello, I am attempting to prepare some 150 PE Illumina data for genome assembly. I saw that my raw data still had universal adapters. In …
Inline barcodes in the reverse reads
written 9.8 years ago by Picasa

Hi, I have a sample of PE reads that I want to demultiplex. For this I used fastq-multx. So for instance, my barcode is `XXXX` …
Best de novo assembler for insect genome ?
written 10.1 years ago by Picasa

Hello, I have an insect genome to assemble (max size: 500 MB) with illumina data composed of paired end and mate pair. I'm thinking to …
Variant calling with multi samples using RNASeq
written 10.2 years ago by Picasa

Hello there, I have RNAseq data and I'm looking for some variants. I plan to call it with the GATK pipeline described here: http://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq The …
Best strategy for de novo assembly with illumina reads ?
written 10.4 years ago by Picasa

Hello, I have paired end and mate pair reads from illumina. My expected genome size is about 1 GB. I'm not a bioinformatician and I'm …
abyss-pe reading files endlessly with se command added
written 10.4 years ago by pepijn.kooij •

I'm running a abyss-pe job using trimmed paired-end MiSeq data of sample with appr. genome size of 120Mb. I trimmed my data using Trimmomatic, which …
pair-end, mate-pairs coding
written 10.4 years ago by kamiljaron

Hello, recently I received quite big dataset of three pair-end libraries (350, 550, 700 is) and two mate-pairs libraries (Nextera, 3000 and 5000 is). I …
VELVET de novo plant genome, strategy question
written 10.5 years ago by dsoronellas •

Dear community, I'm planning to use **Velvet** to assemble a **plant genome**, but because I'm new to de-novo genome assembly field I have a couple …
How to generate contigs from bam alignment
written 11.0 years ago by goubert.clement •

Hi all, I am currently trying to perform a new assembly using paired and mate paired reads. I first mapped my paired-end on a reference …