Velvet
Module:
module load app/velvet/1.2.10-9adf09f-KMER31
Run Software:
PE data – creating & writing to a directory called “velvet_output” with k-mer size of 21 :
velveth velvet_output 21 -fastq -separate -shortPaired trimmed/Read1_trim_p.fq trimmed/Read2_trim_p.fq
velvetg velvet_output ……..”options”
SE data – creating & writing to a directory called “velvet_output” with k-mer size of 21 :
velveth velvet_output 21 -fastq -separate -short trimmed/Read1_trim.fq
velvetg velvet_output ……..”options”
Options:
-ins_length 300
-min_contig_lgth 1000
-exp_cov 100
-cov_cutoff 10
SPAdes
Module:
module load app/SPAdes /3.13.0 (default)
Run Software:
Single library of PE Reads
spades.py -o “outputdir” -1 Read1_pair.fq -2 Read2_pair.fq
Multiple libraries of PE Reads with different ins sizes
Output:
- Produces scaffolds AND contigs where velvet only produces contigs
- Uses three different default k-mers (multi-k-mer approach) – allows for normalization of different read lengths
- To find N50 – very difficult
- Use contigs when using QUAST
- Use scaffolds when using BLAST
BIX King 