mariokostelac

>1
CAATTATATTnAGTATGGAAGATAAAAGAACTACGnnGAATCTGATGTCGCAGTCnnTCn
nGCACTCGCGAGATACTGACnnAnAAAAnCCACAGTGGACCATATGGCCATAATTAAGnA
AGTACnACATCGnnGGGnAGACAGGAAAAGAACCCGTCACTTAGGATGAAnATGGAnTGn
ATGGCAATGAnAATnACCCAATCACTGnCTGACnnAnAAAnGGATAACAGAAATGGTTCC
GGAGAGAAATGAACnAAGGACAAnACTCTATGGAGTAAAATGAGnTGAnTGCTGGATCAG
ATCGAGnTnGAnTGGTATCAnCnCTTTGGCTGTAACATGGTGGAATAGAAATGGACCCGT
GACAAGTnACGnGTCCATTACCCAAAAGTATACAnnAGACTTnAnTTnTTnnGACAAAGT
CGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTAGAAATCAAGTCAAGATnAC
GCnAnGAAGAGTAGnAnnCATAAACCCTGGTCATGCAnGnAnnCCTCAGTGCCAAAGAGG

mariokostelac

>1
AGAGTGCAGAGCAACAAAAACAGCATACAGAAGTATAAATGCACAGTTACGCGCAAGACA
GGTGCTGTGGGTCACGGCAATCACTCGACACAGAAGTATAAACCAGCCCTAACCCCGGCA
TCCTGGCCAAATTACCTCCGGTCCTTACCCATCATGGCCTCCCAATCATCCCCATCCACC
AAATTAGCTGTATCACTTTCTCTTCACTCCACCTATAGCTGGTGTGTGGTGAGCGCACTG
GCGCTGTTGTCATGTTGGTACGGTCACATCATCCAAGTGGATTCTGCACACTGGGGGTGG
TGTGAAGGGATCCCTGTCATGATTGTGGAGCTCTTTGGGTGTATGGCCATACACGATAAA
TGGGCTACATAAATACACACATATTACATTTCAGCACATTATCACTGTGGTGTTGAAATG
TAACTAAAATCAAACTTTATAGTTACTCAATCTCTCTTTTCTGTCTTTTTTCAGAGGCTT
TTGACATGGTGCTTCGTCTGGGCCGTAATTCCACTCTGATGGTGTTACGCGAGGAGTTTC

mariokostelac

>1
TTTTTCTTATTTTTCCTTTGTTTTTTTTGATTGTTTGGGTTTTTACCAAAATCTGGTTTC
ATTTCAAGCAGCTCCATTTTGAATATTTTCCCCAGAAAAACAAAAATAAAAAACAAGATA
TGTTGAATGCTTATTTCCCCCACTGTAAGTAAGTTCTTTATGCAAACTTGACACATTTTT
TCGACCAAATCAAAAGTAATGTTGTACAATGCATTCAATTGGTTGGACTCGTGTTATATT
ACCATCAATCATATTTTCATCAGnCACCAnACTGAAAAATTCTTCCAACAGACAAAAATC
CTTGGGAAAACATGAGCTTTGAAAATTAAATGTGACCTTAAGCTATTCCAAATTATTTAT
CAGGCTATACTCATTCCCTTGTGCGCTCATTTTTATTTACACATGCCATGTACCTTGGCA
AGGCTCCAAAGTAACCACAATGATGTGGAACAGTTATTCTGCACCGCTGCAAGCATACAG
AAGAACTATTAATCTTAGTTTACATGTCTGCAAACTGAATGACGCCACCTAATGAACTTA

mariokostelac

/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

mariokostelac

#!/usr/bin/env bash

head -n $(($(($1+1))*2)) | tail -n 2

mariokostelac

# 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

#!/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

#!/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

#!/usr/bin/env bash

awk '
  {printf "%d\t", $1 + 1} #Aiid
  {printf "%d\t", $2 + 1} #Biid
  {if ($5 == $9) {        # orient
    printf "f\t"
  } else {
    printf "r\t"
  }}

mariokostelac

20| 10 (0.15%) ---
21| 21 (0.31%) ------
22| 45 (0.66%) ------------
23| 76 (1.12%) --------------------
24|130 (1.92%) -----------------------------------
25|200 (2.95%) -----------------------------------------------------
26|258 (3.81%) --------------------------------------------------------------------
27|308 (4.54%) ---------------------------------------------------------------------------------
28|360 (5.31%) -----------------------------------------------------------------------------------------------
29|444 (6.55%) ---------------------------------------------------------------------------------------------------------------------