sickle + flye pipeline sickle: Windowed Adaptive Trimming for fastq files using quality flye: Fast and accurate de novo assembler for single molecule sequencing reads

input_1:FASTQ

@09e78c4b-eb54-4220-abac-b116a84b1082 runid=4de97058536f00a50a5594d603041572795f8954 read=1128 ch=460 start_time=2017-11-05T11:38:59Z TTGTTGTACTTCTTCGGTTACTCCAGGTTGGGTGTTTTAACCGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTCGTGCGCCGCTTCAGGCATGAAATCGAGGTATTTCTCCGTCGACCAAAGCTGCTCTTCCGGCCGCTGTCAGTTTGCGGGTTCGCTTAAGCCAGACCTTTATCGACCTTGCCGTAGGTGGTTTCCTTTCCGGGGATTCCCGCACTGCACGCGGATGGCTTTGAATCAAAGCTCTTGATGACGAACTGTCATCAGGCTTCATCATGTACTGTGACCGGTGGTATGGCAATGCTTAAATGCGCCTTCACGAGACGCGCCGCCGGTAACTGGTAAAGCGGCATGTTGGCGGCTGGCTTTAATATCACAGCGCCATATCAACCCGCTGAAATGGCCGACATCGTAACCGGACCGCGACGCCAGTAAGCACCTTTATAGAAAACGCCAGATATCTTCGATACGGTGCGCATCGCGATGTATGACATAAGCTACGGACAAAGGTGATCCTGCAGGCGCCAGAGGCCACGGAAGCTCACGCATTGAGGGTGGCATCCCCAGACCCGTAATACCGTCCTCGTTGATTTTTTAATGTGACGAAATTACGCCCAGTTCAAAACTTCAGCCTTTACGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTATTTTACCATACAAGTATAAGATCGAAAACTTGGTGATCACAAAAAGGCGTATATATTTGCGCTGTGAATGGTTGACAAAGATGAAATAGAATACCTTTTGTCAGCTGACGCACCCTCTTATCTTATTGGATTTATGTTCCACGTGCGCCCCCAGCCCGCAACAATGATCAACATACCGCAAAGCGCAATCAACGCACCACGTCCAGTCATGAAGGTCAGTTTCACGCCATCCACAACGCGCAACCACATCAACGCCGATGCAGACATAAACGCCACCATAAGCCGCGTAAACACGCCCACTCGCCCGCTGGTTGCAACGTTAACCAGACAAACGGCATGGTAAGTCCGCCAGGAGAAACAGCAAACAGATACTGGCGTTTTCGTTTTAACTCCTGCTGCGGGGCAGAAAGCATCCAATAATTTCACACAGCGCAGTAGCAAAAATAGTAACGTTGTTTAAATCATCTTTGTGTCTCTTATTGACATCATGGCGGTTCGGCGGACGCTGATATTCGTTGCGGGCAATAACTGAATTTTGCGTCGCAGTGGATGGCATGAATCCTGCTATTATTCATACAGAATGAATTATGAAAAATTCTCAACCAAAACGAAGATCCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCAGAACTAATAAACTGGTGATTAGGTCTGGCGACGGTGCACAAAACCGCCAGCACGCCGCTATGGAAAAGAACAATGGAACGAGCAATCTGCGCCAGAAGTGAATAAACGCACTGAGAGTGGAAGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGGTATGAAAGCGCCAACATCCGAAATACCTACTGGGAGCCCAATACTTTTGCATACTGGACCGTCGAACTAGCGCGTTATTACTAACCTGTTATTGATTTGGGAATGTAAGGACGCGTTATGCCAAAGCGCCCACAGTGTTACGCCAGCGATGAAGATTTACGCTATGTACATCAACTCGACAATAACGCCAGTATTGATGCGTTACTGGTTTGAAGGAACCCTACGAAGCCTTTGTTGAACTCTCTCTGATCTGTGTATGATAAAGCATATTCACGATCAGAGCGAACGGCGCTTTATTGAGGGTGGAATGTGACGGCGAAAAAGCCGGTCTGGTGGAGCTGGTGGAAGTATGTTCATCTCGCCGCGCAGAATTTCAAAGATAATTATCTCCCGAATTATCAGGAAAAGGTCACAGCAGCCGATTACTGCAAATTAACAATGGACTATGGCTTTTACCGTTCTCAATCTCTATAAGCTGTATCTGATCGTTGATAAAGAGAATGAAAAAGCGATTCACGATTTACCAACTTGTGGCTTTTCGGTTGAAGGTGAATTGATGGTTAACTTTATTAATGTTCAATATCGTAATGCCGTTGTATTGTATATTCCAGCATCAGTATCTGGCAGAACACAAAAACCACCGGGTCAACGAACTCTCTTCGCGACCGATAGCAATAGCATTAATATTAATAATCGATCGTATTTTTGATGGTGTAAACCCGTTCGACGGCAGGTTTTACTCCTTCATCAACAATGATTAGCTGACAGTCCACCGGATTAGCGTGACTGTATTCAACTCTGTTTTACGGTATTGAACCGTTGATTATTCGATACGGTAACCGCCAATCTAATTTTTGATCGGATCCGTTATTGATGGCATTAGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCATCTGCATTTTGTTTTGCTGCTGGCTTTGTCACGAAGCCATTATCATCCGGTTTCCCCAACTCTATTTTGAAGCGGGAAGGTGAATTCTGCTAGCTGGCATTTTCCCTGTAAACGTACTCTCTTCTCCAACGTCTCGGCTTTGGTAATAGTGGCGTCCAGTACCAGAACGACCACGGTATTATTTTCCAGATCCAGTAATTCCGAGTGAATCAAAACAACCTTCTTCGGTAAAGTTCAGTACAGTTTCGTCCGTTTCACCTTTAACTCTGGCCGATGACGTCACCCAAGGTGAGGTATCTTTTGGACCACGCAACGGATAAATCGTTCATTATTTGTACATCTCAGGGGTAAATGAAAGTGTT

-c "8" -m "64" -s "-t sanger -q 15 -l 2000" -f "--genome-size 10M"

Output

>contig_1 GGGTATTGAAAACCTATGGTGAAGATTCCATTCCCGCTGTCCATTCCATCCTTTCATCCT TCCATTTCCTCCTTCCATTCCATTTCCTTCCTTCCTTCATTCCATCCATTCCATTTTCCA TTCCATTCCTGTCCATCCATCGTCCATTCCTTCCATTCCTTCCATTCCATTTCCTTCTCC TCCTTTTCCATTCCTCCATTCCATTCCTCCATTCCATCCATTCCATCCATTCCTTCCATC CTCATTCCTTCCTCCTTCCGTCCATTCCATCCTGTCCATTCCTCCATCCTCCATTCCTTC CGTCCTTCCTCCATTCCATTCATCTTGTCCGTCCATTCCTCCATTCCTATCCATTCCGTC CATTCCATTCCATCCATTCCATTCCATCCATTCCTTCCATTCCGTCCATTCCATCCATCC ATTCCATTCATCTTTCCTCCATTCCATTCCATTCCTTCCTTCCATTTCCATTCCATCCAT TCCATTCCGTCCATTTCCTTCCATTCCTTCCATTTCCTCCATCCATTTCCATCCATCTCC

nanopore~flye-sickle_se

input_1:FASTQ

input_1/out-20171105_1126_171105_Loman_Ecoli.fastq

Option

Output

output.flye/scaffolds.fasta