Mario Kostelac mariokostelac
mariokostelac
/ ovlstore2afg.sh
Created
September 13, 2015 20:13
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| #!/usr/bin/env bash | |
| awk '{printf "{OVL\nadj:%c\nrds:%d,%d\nahg:%d\nbhg:%d\n}\n", $3, $1-1, $2-1, $4, $5}' |
mariokostelac
/ extract_reads.sh
Created
September 4, 2015 14:23
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| #!/usr/bin/env bash | |
| output_dir=${1-.} | |
| DONE=false | |
| i=0 | |
| until $DONE; do | |
| read header || DONE=true | |
| read seq || DONE=true | |
| echo $header > $output_dir/$i.fasta |
mariokostelac
/ run_args.txt
Created
August 28, 2015 16:38
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| # version: 6a90598-dirty | |
| #/Users/mario/assembly-tools/bin/layout --overlaps_format=mhap -r /Users/mario/assembly-tools/npore_ecolli_reads/reads-nmeth-all_2d.fasta -x overlaps.mhap -v 1 | |
| # filter reads parameters | |
| READS_MIN_LEN: 3000 | |
| # trimming parameters | |
| READ_LEN_THRESHOLD: 100000 | |
| MAX_READS_IN_TIP: 2 | |
| MAX_DEPTH_WITHOUT_EXTRA_FORK: 5 |
mariokostelac
/ nth_read.sh
Created
August 20, 2015 11:48
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| #!/usr/bin/env bash | |
| head -n $(($(($1+1))*2)) | tail -n 2 |
mariokostelac
/ croler.coords
Created
January 11, 2015 23:35
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| /Users/mario/Downloads/results/K03455.fasta /Users/mario/Downloads/results/croler.fasta | |
| NUCMER | |
| [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [COV R] [COV Q] | [TAGS] | |
| ========================================================================================================== | |
| 6487 6744 | 1 255 | 258 255 | 89.15 | 2.65 98.08 | K03455 1 | |
| 5344 5661 | 318 1 | 318 318 | 94.03 | 3.27 99.69 | K03455 2 | |
| 6446 6704 | 258 3 | 259 256 | 90.35 | 2.66 99.22 | K03455 4 | |
| 6499 6764 | 265 3 | 266 263 | 89.10 | 2.74 99.25 | K03455 7 | |
| 9002 9222 | 190 410 | 221 221 | 91.86 | 2.27 53.90 | K03455 8 |
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| >1 | |
| TTTTTCTTATTTTTCCTTTGTTTTTTTTGATTGTTTGGGTTTTTACCAAAATCTGGTTTC | |
| ATTTCAAGCAGCTCCATTTTGAATATTTTCCCCAGAAAAACAAAAATAAAAAACAAGATA | |
| TGTTGAATGCTTATTTCCCCCACTGTAAGTAAGTTCTTTATGCAAACTTGACACATTTTT | |
| TCGACCAAATCAAAAGTAATGTTGTACAATGCATTCAATTGGTTGGACTCGTGTTATATT | |
| ACCATCAATCATATTTTCATCAGnCACCAnACTGAAAAATTCTTCCAACAGACAAAAATC | |
| CTTGGGAAAACATGAGCTTTGAAAATTAAATGTGACCTTAAGCTATTCCAAATTATTTAT | |
| CAGGCTATACTCATTCCCTTGTGCGCTCATTTTTATTTACACATGCCATGTACCTTGGCA | |
| AGGCTCCAAAGTAACCACAATGATGTGGAACAGTTATTCTGCACCGCTGCAAGCATACAG | |
| AAGAACTATTAATCTTAGTTTACATGTCTGCAAACTGAATGACGCCACCTAATGAACTTA |
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| >1 | |
| AGAGTGCAGAGCAACAAAAACAGCATACAGAAGTATAAATGCACAGTTACGCGCAAGACA | |
| GGTGCTGTGGGTCACGGCAATCACTCGACACAGAAGTATAAACCAGCCCTAACCCCGGCA | |
| TCCTGGCCAAATTACCTCCGGTCCTTACCCATCATGGCCTCCCAATCATCCCCATCCACC | |
| AAATTAGCTGTATCACTTTCTCTTCACTCCACCTATAGCTGGTGTGTGGTGAGCGCACTG | |
| GCGCTGTTGTCATGTTGGTACGGTCACATCATCCAAGTGGATTCTGCACACTGGGGGTGG | |
| TGTGAAGGGATCCCTGTCATGATTGTGGAGCTCTTTGGGTGTATGGCCATACACGATAAA | |
| TGGGCTACATAAATACACACATATTACATTTCAGCACATTATCACTGTGGTGTTGAAATG | |
| TAACTAAAATCAAACTTTATAGTTACTCAATCTCTCTTTTCTGTCTTTTTTCAGAGGCTT | |
| TTGACATGGTGCTTCGTCTGGGCCGTAATTCCACTCTGATGGTGTTACGCGAGGAGTTTC |
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| >1 | |
| CAATTATATTnAGTATGGAAGATAAAAGAACTACGnnGAATCTGATGTCGCAGTCnnTCn | |
| nGCACTCGCGAGATACTGACnnAnAAAAnCCACAGTGGACCATATGGCCATAATTAAGnA | |
| AGTACnACATCGnnGGGnAGACAGGAAAAGAACCCGTCACTTAGGATGAAnATGGAnTGn | |
| ATGGCAATGAnAATnACCCAATCACTGnCTGACnnAnAAAnGGATAACAGAAATGGTTCC | |
| GGAGAGAAATGAACnAAGGACAAnACTCTATGGAGTAAAATGAGnTGAnTGCTGGATCAG | |
| ATCGAGnTnGAnTGGTATCAnCnCTTTGGCTGTAACATGGTGGAATAGAAATGGACCCGT | |
| GACAAGTnACGnGTCCATTACCCAAAAGTATACAnnAGACTTnAnTTnTTnnGACAAAGT | |
| CGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTAGAAATCAAGTCAAGATnAC | |
| GCnAnGAAGAGTAGnAnnCATAAACCCTGGTCATGCAnGnAnnCCTCAGTGCCAAAGAGG |
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| >1 | |
| CAATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCA | |
| CTCGCGAGATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACAT | |
| CGGGGAGACAGGAAAAGAACCCGTCACTTAGGATGAAATGGATGATGGCAATGAAATACC | |
| CAATCACTGCTGACAAAAGGATAACAGAAATGGTTCCGGAGAGAAATGAACAAGGACAAA | |
| CTCTATGGAGTAAAATGAGTGATGCTGGATCAGATCGAGTGATGGTATCACCTTTGGCTG | |
| TAACATGGTGGAATAGAAATGGACCCGTGACAAGTACGGTCCATTACCCAAAAGTATACA | |
| AGACTTATTTTGACAAAGTCGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTA | |
| GAAATCAAGTCAAGATACGCAGAAGAGTAGACATAAACCCTGGTCATGCAGACCTCAGTG | |
| CCAAAGAGGCACAAGATGTAATTATGGAAGTTGTTTTTCCCAATGAAGTGGGAGCCAGGA |
mariokostelac
/ influenza-A.seq
Created
November 13, 2014 21:30
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| >gnl|ti|1086975905 name:1099575910428 mate_pair:1086975851 | |
| TGGAAATCCGTCTCGAATGGAGGTCTAGTGCGTTTCCGCTTCAACCCGATGATTGTCGAACTTGCAGAAA | |
| AAGCAATGAAAGAGTATGGAGAGGATCTGAAAATTGAAACAAACAAATTTGCAGCAATATGCACCCACTT | |
| GGAGGTATGTTTCATGTATTCAGATTTTCATTTCATCAATGAACAAGGCGAATCAATAATGGTAGAACTT | |
| GATGATCCAAATGCACTGTTAAAGCACAGATTTGAAATAATCGAGGGGAGAGACAGAACAATGGCCTGGA | |
| CAGTAGTAAACAGTATCTGCAACACTACTGGAGCTGAAAAACCGAAGTTTCTACCAGATTTGTATGATTA | |
| CAAGGAGAACAGATTCATCGAAATTGGAGTGACAAGAAGAGAAGTCCACATATATTACCTTGAAAAGGCC | |
| AATAAAATTAAATCTGAGAACACACACATTCACATTTTCTCATTCACTGGGGAGGAAATGGCCACAAAGG | |
| CAGACTACACTCTCGACGAGGAGGTCATAGCTGTTTACTGAGGGACCCATTTAAAATTCTAATACCCAGC | |
| TTTGAACGTGACCATGCCAAACAAGGACAACCTGACCACACAAGAGGTCAA |