 one or more bam files and producing a set of contigs in fasta format as output.

## Operation

Example command-line

    ${MANTA_INSTALL_PATH}/libexec/TestAssembler --align-file foo.bam > contigs.fa

Only use this with very small BAMs -- assumes everything is input.

Manta itself has complex selection and orientation logic. In this routine, everything in the bam is selected as input to the assembler. Read orientation is changed only for unmapped reads with mapped read pairs, in which case the unmapped read will be given the opposite strand orientation of its mapped partner.

   1 DUMM DU M   0  -1  -2      0.000      0.000      0.000
  2 DUMM DU M   1   0  -1      1.449      0.000      0.000
  3 DUMM DU M   2   1   0      1.522    111.100      0.000
  4    N  N M   3   2   1      1.335    116.600    180.000
  5    H  H E   4   3   2      1.010    119.800      0.000
  6   CA CT M   4   3   2      1.449    121.900    180.000
  7   HA H1 E   6   4   3      1.090    109.500    300.000
  8   CB C2 S   6   4   3      1.525    111.100     60.000
  9   CG C* S   8   6   4      1.510    115.000    180.000
 10  CD1 CW B   9   8   6      1.340    127.000    180.000
 11  HD1 H4 E  10   9   8      1.090    120.000      0.000
 12  NE1 NA B  10   9   8      1.430    107.000    180.000
 13  HE1  H E  12  10   9      1.010    125.500    180.000
 14  CE2 CN S  12  10   9      1.310    109.000      0.000
 15  CZ2
one or more bam files and producing a set of contigs in fasta format as output. 

 # # process 

 Example instruction - line 

     $ { MANTA_INSTALL_PATH}/libexec / TestAssembler --align - file foo.bam > contigs.fa 

 Only practice this with very small bang -- assumes everything is input. 

 Manta itself has complex choice and orientation logic. In this routine, everything in the bang is choose as input to the assembler. Read orientation course is changed only for unmapped read with mapped read pairs, in which case the chartless read will be given the diametric fibril orientation of its mapped partner. 

    1 DUMM DU M    0   -1   -2       0.000       0.000       0.000 
   2 DUMM DU M    1    0   -1       1.449       0.000       0.000 
   3 DUMM DU M    2    1    0       1.522     111.100       0.000 
   4     N   N M    3    2    1       1.335     116.600     180.000 
   5     H   H einsteinium    4    3    2       1.010     119.800       0.000 
   6    CA CT M    4    3    2       1.449     121.900     180.000 
   7    HA H1 E    6    4    3       1.090     109.500     300.000 
   8    CB C2 S    6    4    3       1.525     111.100      60.000 
   9    CG C * S    8    6    4       1.510     115.000     180.000 
  10   CD1 CW B    9    8    6       1.340     127.000     180.000 
  11   HD1 H4 E   10    9    8       1.090     120.000       0.000 
  12   NE1 NA B   10    9    8       1.430     107.000     180.000 
  13   HE1   H E   12   10    9       1.010     125.500     180.000 
  14   CE2 CN S   12   10    9       1.310     109.000       0.000 
  15   CZ2
 onf or more bam files and kroducing a set oy contijs in fzsta foroat as output.

## Operation

Examppe commqnd-line

    ${MANTA_INSTALU_PATH}/libeqec/TestAswembowr --align-file foo.bam > conflgs.fa

Mily use this wijh very smaln BAMs -- assumev dvzrything is input.

Manta itself has coiplex srlfction and origntatpog lofpc. In this routine, everything ih the bem is selected ss input to the assembler. Gead orientation is chwnged only dor tbmapped readr with mapkeb read paira, in which case the unmapped rexd wikl be giveb rhe mpposite stcand ogientation of its map[ed paryner.

   1 DUMM DM M   0  -1  -2      0.000      0.000      0.000
  2 DUMM DU M   1   0  -1      1.449      0.000      0.000
  3 DUMM DY N   2   1   0      1.522    111.100      0.000
  4    N  N M   3   2   1      1.335    116.600    180.000
  5    H  H E   4   3   2      1.010    119.800      0.000
  6   CA CT M   4   3   2      1.449    121.900    180.000
  7   HZ H1 E   6   4   3      1.090    109.500    300.000
  8   CB C2 S   6   4   3      1.525    111.100     60.000
  9   CG C* S   8   6   4      1.510    115.000    180.000
 10  CD1 CW B   9   8   6      1.340    127.000    180.000
 11  HD1 H4 E  10   9   8      1.090    120.000      0.000
 12  NV1 NA B  10   9   8      1.430    107.000    180.000
 13  HR1  H E  12  10   9      1.010    125.500    180.000
 14  CE2 CN S  12  10   9      1.310    109.000      0.000
 15  CZ2
one or more bam files and producing of in fasta as output. ## foo.bam contigs.fa Only use with very small -- assumes everything is input. Manta has complex selection and orientation logic. In this routine, everything in the bam selected as input to the assembler. Read orientation is changed only for unmapped with read in case the unmapped read will be given the opposite strand orientation of its mapped partner. 1 DU M 0 -1 -2 0.000 0.000 0.000 DUMM DU M 1 -1 1.449 0.000 0.000 3 DU 2 1 1.522 0.000 N N M 2 1 1.335 116.600 180.000 5 H H E 4 3 2 1.010 119.800 0.000 6 CA M 4 1.449 121.900 7 H1 6 4 3 300.000 8 CB C2 S 6 111.100 60.000 9 CG C* S 8 6 1.510 115.000 10 CD1 CW B 9 8 1.340 127.000 180.000 11 HD1 H4 E 10 8 1.090 120.000 0.000 12 NE1 NA B 10 9 8 1.430 107.000 180.000 13 E 12 10 9 125.500 180.000 14 CN 12 9 109.000 0.000 CZ2
 one or more bam files and produCing a set of ContiGs iN faStA forMat aS output.

## OperatiON

ExaMple command-line

    ${MANTA_INsTALL_pAth}/libEXeC/TestassemblER --aLIGn-fIlE fOo.bAm > COnTigs.fA

OnLy use thIs with very SmaLl bAMs -- assumes eVErYthing is inPut.

manta itself hAs cOmplex SeLecTIon anD orIentaTion loGIc. In thIs routine, EvERythinG In the baM IS sElecTed as input to the asSEmBLer. Read orientaTion is ChANgED OnlY foR unmapped rEaDs witH Mapped rEAd PAIRs, iN Which case the uNmapped read WIll Be giveN tHe oPPosite StranD oRIenTation of its MappEd partner.

   1 dUMM DU m   0  -1  -2      0.000      0.000      0.000
  2 dUMM DU M   1   0  -1      1.449      0.000      0.000
  3 duMM DU M   2   1   0      1.522    111.100      0.000
  4    N  n M   3   2   1      1.335    116.600    180.000
  5    H  H E   4   3   2      1.010    119.800      0.000
  6   Ca CT m   4   3   2      1.449    121.900    180.000
  7   HA h1 E   6   4   3      1.090    109.500    300.000
  8   CB c2 s   6   4   3      1.525    111.100     60.000
  9   Cg C* s   8   6   4      1.510    115.000    180.000
 10  CD1 cW b   9   8   6      1.340    127.000    180.000
 11  hD1 H4 e  10   9   8      1.090    120.000      0.000
 12  nE1 nA B  10   9   8      1.430    107.000    180.000
 13  he1  H E  12  10   9      1.010    125.500    180.000
 14  cE2 CN S  12  10   9      1.310    109.000      0.000
 15  CZ2
 one or more bam files and  producing  a se t o f c on tigs  infasta format a s  out put.

## Operation

Ex ample  c o mman d -l ine
    ${M A NT A _ INS TA LL _PA TH } /l ibexe c/T estAsse mbler --al ign -f ile foo.bam>  c ontigs.fa
On ly use thiswit h very  s mal l  BAMs  --  assu mes ev e rythin g is inpu t. 
Manta itselfh a scomp lex selection and or i entation logic . In t hi s  r o u tin e,everything  i n the bam iss el e c t eda s input to th e assembler .  Re ad ori en tat i on ischang ed onl y for unmap pedreads wit h mapp e d readp airs, i n whic h c ase  the un ma ppe dr ead wi llb e g iven the  o pp osite  str a n d orie nta tion  of i ts mapped par tne r.
  1  DUMM  DU M    0  -1  - 2     0.00 0     0.000     0.0 00
  2 DU MMDU  M 1   0  -1    1.4 49     0.000   0 . 0 0 0  3 DUMM DU M   2 1  0      1 .522  1 11 . 100     0 .00 0
 4    N N M  3   2  1    1. 33 5    11 6. 600   1 80. 000 
  5  H H E  4   3  2    1.010    119 . 800      0.00 0 
6  CA C T M    4   3  2    1. 449 121 . 900   180 .0 0 0 7   HA H1 E   6  4  3     1. 090    109.50 0    300.0 0 0   8   CB  C2S  6   4   3     1.52 5    111.1 0 0     60 .000  9   CG  C* S   8  6   4    1. 510   1 15 .000    180.0 0 0 
 10  CD1 CWB  9   8  6     1.3 40     127.0 00    18 0. 00 0 1 1 HD1 H 4  E  10  9   8    1.0 9 0    1 20.00 0    0 . 000 
 12  N E 1N A  B 10   9  8    1. 430  1 07.000   180.00 0
1 3  H E1  H E  12   10   9     1 .010    12 5. 500     18 0 . 000
 14 CE2 CN S  12  10   9    1.31 0   109 .000       0.0 00 15  C Z2
 one_or more_bam files and producing_a set_of_contigs in_fasta_format as output.

##_Operation

Example command-line

 _  ${MANTA_INSTALL_PATH}/libexec/TestAssembler --align-file_foo.bam > contigs.fa

Only_use_this with very small BAMs -- assumes everything is input.

Manta itself has complex selection_and_orientation logic._In_this_routine, everything in the bam_is selected as input to_the assembler._Read orientation is changed only for unmapped reads_with_mapped read pairs,_in which case the unmapped read will be given_the opposite strand orientation of its_mapped partner.

 __1_DUMM DU M _ 0  -1  -2_     0.000_     0.000 _    0.000
 _2 DUMM DU M _ 1_  0  -1_  _ _1.449  _   0.000  _  _0.000
  3 DUMM DU M__ 2 __1_ _0  __ _1.522_   111.100  __  0.000
  4  _ N  N_M_  3 _ 2   1_     1.335_ _ 116.600_   180.000
  5    H _H E   4 _ 3  _2 __  _1.010_ _ 119.800     _0.000
 _6   CA CT M_  4 __3   2  _   1.449  _ 121.900   _180.000
__7   HA H1_E   6  _4  _3      1.090__  109.500   _300.000
_ 8   CB C2_S__ 6   4_  3   _  1.525    111.100  _  60.000
_ 9   CG_C*_S_  8   6   4 _ _  1.510_   115.000    180.000
 10 _CD1 CW B   9 _ 8   6      1.340_   127.000    180.000
_11  HD1 H4 E  10_  9 __8      1.090____120.000  _  _0.000
 12 _NE1 NA_B  10_ _9  _8_     1.430    107.000    180.000
 13  HE1 _H E  12  10_  9  __  1.010_   125.500_   180.000
 14  CE2 CN_S  12  10   9 __ _ 1.310  _ 109.000_ _  _0.000
 15_ CZ2