From 2b2bf9fdbaf1cd1a50145971e9d5d1fa54a9fa9d Mon Sep 17 00:00:00 2001 From: Brian Ondov Date: Tue, 10 Feb 2015 17:52:14 -0500 Subject: [PATCH 1/3] Parsnp logo --- docs/content/parsnp.rst | 2 ++ docs/content/parsnp/parsnp_icon_medium.png | Bin 0 -> 18123 bytes 2 files changed, 2 insertions(+) create mode 100644 docs/content/parsnp/parsnp_icon_medium.png diff --git a/docs/content/parsnp.rst b/docs/content/parsnp.rst index 2363a82..a41e7f2 100644 --- a/docs/content/parsnp.rst +++ b/docs/content/parsnp.rst @@ -3,6 +3,8 @@ Parsnp ====== **Rapid core genome multi-alignment** +.. image:: parsnp/parsnp_icon_medium.png + Project home page: https://github.com/marbl/parsnp Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. diff --git a/docs/content/parsnp/parsnp_icon_medium.png b/docs/content/parsnp/parsnp_icon_medium.png new file mode 100644 index 0000000000000000000000000000000000000000..7bf9da655b47b0e4793c917d71f44579b5fe161b GIT binary patch literal 18123 zcmaI719WA<(=U2r+qP|cGI4Sywr!knVjB}%6Wf^Bwryu(>(2lCF5Z3Xt+&_e-QCso ztFEfOcdy;m-4Q@VDI|D&cmM!^BqRMz`CktDmqK8n|J@^1H!}ZakQQPJVgNv09KyR1 z)W15ZiL|l;0N_Op0Qd(30I&Z@{wDx{D=PqSW(WZArvU&sj#=$L1phU_IZA7}002CC z|4CqY{@?!ba7c(a_E4eT{DJiL-v#B}1^0)8*6aKFz zL~aQJIr6ixxVyVEyK^u*I9sr=@$vDou(GqTvornUU~=)a2N`)V*}G8uw~+rO=bM>} ziL;d>$jZT<^gnWqj2&D-LgeKC>F9r7|E(v;%KZQIWbg7n&H85`%YRx}*qB*a{=Z=V zjQ!vG{a+{#Bgg*+{g+k$-I?HjMDZ&*Tbcb+_diMrvkCr}`2UOcf0PsaC!Jry*~|#! z;H>K4U@QC|4_MjTxR@9@n*GNQf-L`Uj{gZ3WciP|{}1#3+qeHk{pVa^_=7Xsd?egn763-sc*(2 zHF9Tt!Z?5<5!yg^p?ldx?=WSf*wWsShd3V5vgfqrIgWPGk)Bi3x4I^vv#O=ZOb<_Q z|DzW@LfsDfE(L?;oKz18J*41O7XP4tx6d*jqOX2=sD`XxSvH%soJFlyA*iw)%p!#* z_Sx%EYnONxLQvV;TfVrx?cnOJQR&=f-lWFQxOf@CAykCjN9JyBKDOEUGpl}a7Z18q ziZLJ|_gz6y(|5~>;@VR~_j`!>RxhZcb(ACDs(^3Pd$$+FI`!HM;vh-M?BM9@?G+7%wOsi77kQmXab#+B-pyXH;t0ojY2hG=Aa1y-+Eqy1fj$4M$=b);w3?e! z=!byonTMUV?BYxc*m7{vwR+VO z1t-yBd65?=3K$I^VyuWVbDBs75cOuAz~N6^C=7 zN^cj^?*pq6i=ACDr%JB*<9edlCU;Jz!jOD=|GLOnE0YW(dn zyWGpHQVD;K=cj3e$)}w2B+kpPv^-@Fl0@Xt=r>$?)S^Qg3+)%$>es14;a7q*uTqq zL|RSeY9Kv+G~xl+OhmqX)yXO~_(5lLUtz!7p8Q0q?YGZ360vMNkGIaJ?cKj3+*%uT z`=WTK@PfU1@S2zr9QB#^_2O+aWd%QZs)zOi$56Ws|#>*8)T-ZSI5MfpQ~Gx{ApW< zu2EcET`l9)t=3MiMUO~QDf?Ds?6l^4KP$C(v!7@?4FcT8_RwrSbv?Olxh}`uJFKv_ z7S}jTuBp=3F&kUJ5OMt(b8``j-EWra%SZJB-wB0D^=c{}GXr&N+wmtd5DI!)?}c4? zZj%T*-=D0Uo>#9M)@aTD@IJ{uzS~hUj2VOu+uvyl8n}v&W*LV{Zm5I@D=^faJCb=UWTfOi0no=ldy(B zSdqMnD^9iuvSWwvAs5$WWqp5fLhB9Q#|j%tC7^!rfu@u`p6&h~i09+O7oC@>&bj8j zBqYrL-H*G1*JfG&y;wKd-2EIC_oV-nQC0C% z(;9!SZ|6+Xqqe*)jp2N35Nn2ETp4oNt%n;juEUtwVA?#ArK9#~L}Tkc_UqLLi1qi+ z71Cji&t)Csp5cMcITS=P&ZDw!E%E;3R@djNZwX5lB2wi!+~BX-5fR_xuhseaE-Fg< zRbR>Jn$O!f6n)RboujRsSf*J^OEq4?zu$AO5W^(wfQlQgdLSROpf;2Ii1u=gBpWP- zMe90!_l6?lmwRt&KW}eux93rdN1~U@uTQNlWIylg8_xl_a=g$~aIE)~ zt47N45}Kki3`9H}Btw}iU3We9#^wegWk=QLD1!~jfRpvl=O*LAd~?_5Bf(zX z3N@lu5YW_}6CYXUVlg-t{`OC&21WpHGda9zB*;~bL5+1n?Yf&=SR_}d^=fBEh2$;B zfq2b#o@th+dpD!{;e7e=;qeji_xvc=%{RmzNmkvpOCWcsdTjMTMr^A}374im(j;$_ z_GzQeB#F3y*>AAe!x>~K873I00*qd8vO;X!IR*jrC}ke&`}+lsuT!3{Tw)Qo zuRr!oJ}>7=Q$_RT@uRxDz?g5g4t!HHnGA+R^U2wl>jM3m+;-tfvM<*>T~6Vo{N1;5 zPqrT0(;H6fJ!e}w%BKr96baAmn&fE8gc;#3Sb3@yxPzw8#zgdB@$6%1$RM7A>_`dH zqX4w2AKU^E$85Mj;Y5~6mLx?brU7)bjYk(n3*bA|fS!`@J6T$BwB+-qPt`J4T4My{w@uX5FjgVW#7%QoU%^A6JcZc>=mNy&4;{jgFG0YV zTHpTZb8(luJ!!A|7T4|ZmSXVMleslNzwYTyp0k3PZ?>ae&q%86&jC3ZmN$*cf`Z>* zl+Cq~p=wxm%>`1n)VA%dHySyC$!9Gt2p^!MvHV6HBkU60kIUGfHU0osBKWk>TEt%T zdvSfZ=TqMoRGCB#7Pk%1V@6@73@qH2kCN0(XJ>S4isn-$Tq53hv98tGS z=@!L{QekbxYR>n>={w({p&ct{-x8aM&aUQw*TJk_Zu_0x*F)4(*Td0!(6*-+d%EhX z?vw$olQ;_a*ei&7p{&>-(3zR$)<2xANpza%*9eU7-?0S)zt8yB8J6wVLk7RM#O?+o zyJJ7gEBVUu8{bORvff+Tc>lOr1PFRSwd&?XU!b->iv~UJE;&8AQn_Zmo;RV9;A*jP zL}O%M10!aP7)kA|vAP*YhsLm;FDG4oS65y*DklB!;{s0fW-x1o$%#Mo*ik)md_IK^ z0l7<@4-hC(RmUj(;!1n)CL;wWpqx*64C*R`PJ<;Ba}U?}L0dg~7h#0FZZD$A_0G-9 zWy8zbV~*Uf&-<#DuJ1$w+%o67@Y0ys>)AFgTj8VeIfjvD;1dU5pBqLGry_54nZECr zH7}ii{~k0kLnnzd>m>d`VnBS$!&>B1ZO8op82>m#;F2$@ZHy(>)D;g^nP5Va89ejY zyuQtK(liCf>QA1d*>PVu~6DewC`08a-T=bi>B?UK_ zJ>UFpF`);byoHj^b~$lNNL!Uue}KTjlhbom;Sjqu1q;3zl*|g%B;9uf^+{37(W6Ir zs7EH(IpqKD+sW95C>-E4H}d6LI%S&`Yd}tTB(P$JkTYI6a11FW6ADtR!Y|JHTYbN? z!~m`MK1xGE*mXB$v#{Hb+Gtb+t?JC5XoTTM4L7Geg@XebJumRIC4f4Zb^3nxR&JV&cgEn8UCTBWj`9yn$1-Usoq zVmd~sMZF*kUCRf&nOS) zzTr0cCw?_~94qkza1T06~9^`4^JdDHK& z7S`&o%yHFCFDUIY-WkMu&Co`ylg7Ym%^&HEs)kKv)t?Xa(QWZhnXfsC64@|mF!&+y z2?)C0qLk=)Ch4eXPeTuEW40LZFqAXBtT0b`7?O3U3>0=f3$hk%h)uRS{-Rwl00}Vl zTQK(CWOnfJ5d0+ZxX}>o>GYtN_AWdwA>fB1*y$#|z2a)@c~Y%VtC#EW5{&ReerAsE ztL5`!X7g{hgL)WrU~FE;$WRFREP0j7%}-`gBr-hyt3Q5n2Nm0VdVbdp4jm?H4)0qV zw#0MGJ%xd{kC>FSj zy>6xkuwMO<&eAsbTfQ%C87qk{jrB&7v(a2TurM+tOFJ!F^^&NfZUuge#@Yu?XXebU zd@Q0$3Y_5()xn5&zy{$VYz$q!spI$_Qvnq&$A1+PP*f~wT=-*BL8-j#1_O3@@qHsY zBR5@j9)o5_3BL9BB0D4i$^eP-s>ZU+cDQN0E%5Bz=Fi_2;rD6=;?Lc#>*n(%D&y8a z;A~8su(T{nE9`S)Oi-oyW@a}8+_V-~bu!#D$>Cu&Rmm%FMPiD)Gd#<6t+~M=_zoPC zo+v!OU%TRdEBuW{RQZeL&w(Rh%h=6YV@{(~q1rBYWNeb%9-6-lZlb862txJ6iae)} zuF|Ok(kApXx2$ez>mMmH2kSC3Izd6pn=$$48>kWI|b%sMTqz&E9)0F8O7j zY5H_p8~9|)x;a1z%5Vt?fs2IB0*Er#?)VW7Ma2(xYb)km5oidlM;|>-wp#4F(Lxfo zx?&;irzdOWqBF!K)ol!|mgM*%jkAcNin4K@CX^fK{Bg{Vv5sB8kzt283jC6FVVy9m z%Z`^|$pLPD*Z}D5QCea5LegJ}3E&R)$mkkL1^A@@)Rrr=)i@(Glq*k^f!Ym3+e`Bw7teZ7@jJ7HoId-&JWb@YXi2PoZ2osRPA1;^i zV3poHX68~mK!>G(R0?{6o|x2ig0Te;GV7?qQPQARHNTYv9sG-#XodWM4@#qr?r4Ou zQG%#H8@&FZmbvuQg$+sMa+gkyE%jq#EzKxZmP--AR9V4DG@}?j`<{x|gVn^r?*qTO zOZS4{pcMflel|>sJ{$`eT41ddTV`$aO(7-+nDu5^$DP!(tMVpFh{OET%}}>j$i&_V z8Jn;CsN{R?xejo1^Rm2C2&t>lyYjCY)nxw0NvK^r`viPiqhKBK1!k|f4I$G>y3}-= z${1Rz;!u1C>R1qZaILwvc^y!EI1AkHTy?m-qP9m4j&2zWGFHDDNx-OVN^B7>iV6GH z8d-vEJ)SJfJ4TB5#LQ_x=MTGleWy^@XN%u{_Ia+aJ?(o2!z*8$^7cUZmSI5Y0A9|n zwiYb|w}8$5P|PF87rSZMy^@=$%`#}Y{O61SA3acdg+YhQ zYP^VErg#aF8KVHhN|V>?nS=yQMDP?70aXRy!jistv#DOieLb21K3sk7 zE!jOhXXJRhwqiRUXSX9h)aM$Xy^t~N5nMlgD20$0x3{Q z$kwhCP-W4%dj@KecFaclUZdXXA<2SvAB|BJ>~qP4Lw{+VNzUTOPEh|iN(;a z54SWTohWV}tTUD$J<9pu)#Go&NQ`FS!q_K#{0-~$O zvFOF?xM_3xS(9vBN}y%;6OoV5aM{Ec*wsg2rY>5WgOEa5MWgTc(=7>3ex$~S4@48t zG2%Ik`R}IO(dgO{myrun3%jA_FWzQqceGThTWi7|s+HStG}F)5Ix~YnG?WBo)Cogz zw%QUDjB-zv8buqB_IB*$NYiGAGeJ_ajxv&bWn>rLrGKXe_%U1Jq9@Gx`G4)UwGsX- z(oMjrZ$|rpFhMvCMaiLM5xf+NL~ud!>BxexCcv+vv5%WHmb`vZ=@UY~4q*sC-gjMk z4EO6ahuAhIic*^ahjGKv@!}VJSS=9@339U0;Dkha$Sw+}E20&lzLP*Or=oQ$pS;aV zhD5rJ32}`5Q2sBQq>y#=aT%+Mc(RnLJ+Ct0_9gfl~ba~WPb{cof-Dx+lXDtbW7u=u9P zU1AI9Qbh3R-gVbX++>7HGrP%EqEVAP+gS33XQOr%4-c>Gi?CKepY9TJluRkK9d} zPX&~nkDo{hj}%^bYpPD*s4*6~XSAN=&!B|*8nYpG#=-L9s#GnHF*n$5wAwV}&xSp` z8}#Zzt<#&b^7y3;`l$*9k75Fg(1w5uF!2#^xs5$l=Yt#?@w<*cXQ6+yYLF)u)N+`BhUo%*VpH5|bpkNT*IhY0dPkd8+k6 zkTI$)(NJ0p2ZtDaiE>NLY3{)CW=uGUNl(89Av3CH1Qs>tyBw$q_Le2ot1J>)S~WDP zTEYoY5yxrU{0j^HI2kZL3DK6t&*}ZHfk{1L=RE1pjfH?g7@G2evHx@ZOqw#7Z0`HK z5u;$SSKpZR$l!pn==ADs8=z=I^JH}2=VFQy`q_~evssV6L=#l$f%rsC8HoOy3qTn~ zyfL>>#hEl{g!}a#KLC&xom--cB4Q414TJ(JLwi+cKco<5TKbPXic*Rd76yizM)hz~ z)&evwaNkB3t<^(aQ%eNdYR2OkOm|>%8nK*q)aXo1M51-b2m@vT9`E|%sIf)0yLlxz z#J2OXb}~P23)kJ$=QgTdm&ZA6jsXHMIz{8GU|KP0czAhW=gJr?25l`B8{T8m1P zDAE+=TEhbMfk9}D0y|||+6dy>nc@W{+Z;ZVa3!qPke@q>mx_p;ulK;fQ=5*22rzI`wYo~%QE zsa;5)i0`=?E6+DS!qob<9`!r?>U|QzfP#pZ+6aBJEl)&t-cTTT(*QfcrANFcJcR~r zG~hwb>am&K<#KpOsdak$cLPDF4iCfplrA3{p z16|DP#bLf?`rrZ`ODn(iC!OoYI?Ztz$Hj%baNa6;BSn9j#PvfXVN1OTVvB9G8DYfx zFEjQ>lzl71Jw}C)f@g}6IWJeHZQ@FnK@iC{G|P=swA5DUH+W9r%n-xvFA?MqIz4Th zZ@`p2h_Tfc{_PoXt($CJY$)Fw(tYIq*FcF_b&qg@yUl(kJG4pRkEt~wNtTIcOp2i6 z%31xUGb3inR7h^r;Ex}1A8WGxX;L<>%vYW_uiBF=5})(cbf!w!$05I#oVusT@sm6` zLuEC17KlkqGYBcd7$-WK$(ds0utZF^ZeCli!98<}XIA_!Q%$Z#@)HN=h4BG16znMMH?4JbuOOH6d|E z(u9m#4bCva00G1O2IczIN#>HcoMT&21P1@sREx-uq5GAk2H4*PQ5bVaFiDdvN$pnh zM31@W<3*40;Nv2uQeX8I;GPTTJ+>3G(XOPNG(y?WjevIu^y$kQ{m}4kkz?L-1rA!A zB>fJ2`LGn&+Ds zRBGrD7w$Y;&KR|EuQW&`X4m~n2Nj@@OBz%1jvZ-<3C_s`3#$M?Hr&af?r(ADtKijK zkQ5_B^Vl6(isY(eoOqx-bGqBNN~Q@3`F?K;U=cyOLKQCR-bqB)AYEy*FT zA^K1qbIc@#wNDp(Ug%c?I8JYYbeQfrrIX9wT8T6VF3xmHmx?vAm+ehwE2$2T)9b%m z8W(Wx8at!Pa>g$)el!Q~AmW=lk`22k8WCdmdkifzJkw4=C_A`w`D2N`XrlaF3}KA* zdi@eaTVbAT3UQDg&L^PIWP^~K-dzwLyk6TWh6a(|l@Md`!f8Sgy7KW)Ty>UuHT!o; z4MJRy|L%gN6tu`-vx1w3qK(+_c?-36-*D>u5a_;3pRb+Sl}>8l;;wgOdxj1iPlVFN zg(BI?80T(opuLPTCWocMmwq#bz7@pJ-ak~KYiE~y`21<+D;$-l>mZ`>R}w2H|CTMI z#Bh}>aLe>clL1$A7t9EeMIY-(4atR6iA5Ts)!r&VMB#HH8&{Uc%-ZcP8*tx5p)%ZO(miPp*7;vv{-sD z%aB_qQ0VM2672cEGG&wXG}CqHOluvGR1$6GWsi&tb_pVfyO_?FH#Rm(36Rw`zY)5_ z6ArJ&9?x3MPznIF3heUOxa%C@>yO&kO_IfX`<&W17%{zzh#)Q6ivVU+{3>nDF2{AU z4mz1W+kd`>V?#nN%4nM-9Q7{D*;TJ|8Ua}e_vJDJZ#OHuUX2`N%DxK(ygGB11r5km zq_c;i`KBI7qDJ*0VLUsIzmpVHZ$RbM*E58FblY=?!OKiDBDAC48*wRBrG13rj zyi+?yg1^vSzv9h>T>7aGQf&JpIiD5b4Y2dW43pc^M z@V{{BFf__vJ>jeuY%cglcRQxlSUPH$L6xCs3H~ruxxWYzv&(3=4>q*0qS#^Jg?M{& zK&+n2tw?@7fll|q7n52#kFV=oR@!_IZf|gHe|Aty$aa`+tY1=0B~(L@bH@npe76t3 zRHj@O87UcM8Ry-Td5Jp>C%MOkb1wVSC?ELx_+&r`ZRBd(?61dHfd{M+gRatJ5M8Zz ziY71+a5PLase0JvWnQG{VAMsJ#C+;LU`Bb25Kt^Id@lcF#n`!%-@8 zd4E)Re|@y5cRzLN(L7xWed6_vmcg4i2r)VlRB%p+6(8d_Md6BR^-RK8)3M@nhJy1& zouxM(ZS1gM)7hEGu?Gj)x=2`?K9e<>_v@86*a&fVM*+>Twr?%_>qAR~?w86=Ml^); zAMGE}oY#5qhhFyFY*QAm@fIV<2nk8lwX)hK_c_4YJP#DI)f-HPRoMi}=OQX)Y0Uaz zQsGw*xQoCTMa`AO*DWQcx6gWZM?XeJjGwB)X)LHFaxpIgnIc!TCFC-k9!6 zTA|^yzNiMl^qZF;m(TZat3jM!^%)&MWL@Qp64DL6Xm@28xGedTh3Qq^2+~PHLokY) zRBbH81-q0N+I^?mZ&j<@DJpu|r{{5zKb*BHe@Udr&QQ(1yrWO=sZ%k`KfLij@InK4 zrHl^ZRHgP;ad2d^ykFwDT|tOFESz`?qu2Q##EyZ^yW^=LvXMLm8CO?fMvGeNTG52+;-O_S#Q3{5O}>hJ@$d$m4E9 zqD88k664DZ9`1l3rKl~9#OHfS${_U7MymW7b#^j@2F#+^^JPYHzSB?Aam2FV;v7); z$t`A!rQ+w+Ch=!4$|KIuum!TN-)5+*o?e+4c7(%8W9O3LhX8=)Th4crcWh1{w?}FxaUjpW^Ab16iN*)B6 z3L=g`wpd-01isTF-RUW8f{GGl-(!M_%iGsv_s^4`Ew<;Q7am4N_)2w0Y=H-&qisE! zba>Xq;f#k<(6r~zdysgJ&Bgsy@*mZIs@-$^KELe-bo<>8eyZ6?V0klPUlx0{-=t%l zruzFEzKU7`UA2dG0#2827=eIqSvyuW2JG~y^_urtsvLhq#oI<>}uRlX4_Sn>gWihcg?4pJ%wjcif+$Ji1O2khvFqwd1?k%S=9M zJr7_9O=u@n02)An+I+R1-F2+G#@;b77hsR_cH@FOM>Y1D#sMmS%`1J-99l2Ei zG@!45i#HzbOM!4<$7(iM;doh?{ygiC+we6}I!ZsrDZc(jZJ7H{EnLJA4boudMeCvrGv~CA zt`!sNb5=@#dmmO1C1RoC+c#NlGk9A;`NI455^;)dus?3hHULG#vVhp+W&C}}dBYj7 zsBCqLI4!9W)t$Dpcggv(cDTO%>2+LT;8QKg*H&vYU))vUkHF8Mg{nlvk=h(ygu-gs zB%bF;9LZb(gmfX)Plg3+1X2dDLIZYh#>g}(3n)31oHbKa;@hKYk&Nursq&6qbcqv! zu_Q>fDX}?A4M5ilq5L_~3rZ5&p!ifoda6CHLRWi~@em1&0SxRg2dOnG!spMkmN?)2 zQ=<72hweI_yXS^P7vAKweqWDkH%ZK4S;tAI?DhLUgrZ0svV}zp^4`FgO=17Bt0yf9 z2@KAt+unYPX}zD9YfpxF0Fy+xU`P0_*Y*wsXt~)Y-3p7&a2Jo5!JCinZ>c;Nw`y=# zSn$ZRX&5inG$L5BV4|sDx*bU`gt9aIfRLVpQRc15!~AvzMYw z7jIldn_lMT9pf0oSbeGunuio^p%h@=hPRtn0ES*2<(Dy@WQ5Z7jR3TB3sV&4B$5|Qqk ztEFW%XxnF5x%4JP-j`)tJqS@bwO>hsSZT36obwh1En>W8!s#`?mKa|M4Yu*!X2uJ< z2XQ)pdnB`h!>*`RDpqvYV=Amu^)`eoFZ>UgAiug;s+GITlxtorxnAfD>HIGjRx1w_ zb}$s(o*tMS(1bCwpT`&lHj>u#Rl4uzgS+3G4Q*zdvxM{GilZ;|o~h$;Puu)PF)+21 znz;9N^93MVZ9Bj_p9kjybb7$7WEJNABE%sE4JlI^DT9Tadz0N47|JEjyyA}3JW)J= z6YU@hmsWfgf)5sQpf5PpGW{4HW*syxHSGwC=*GaPzuC#LVS86SY?2O)6bXf5l)FBO zZI@xkR3c3%0ekET$%`g4Kp5TDOsa9Gdzh$>pt1M3Yv~H6<=**Y;eL^xDKANWhie_< z>P&_SIq!h*0+P>NOgG!niqOWy|Hz1^q_*ELGVHh!B3SJxTK1Y;47%#;WwhUvz!eKy zBKzUu&}xc*a2vM>4BJmDlTfd;xXqZKa5$*jhA)cRq^yW%nD`jY^}RQuS#T{^WmEv) z5Ij=Jp!@vw3#(6O;kiMxhdZnBOtD4!ycJ=Gc9_qTs7qF!2h1I84wE!y8TYz`$(YQ> zx;W|Oc=&s_>ywhuyHJwSMthaX-?Hq6L|nQf_`~{DH0!2%E`R*yV?=^q*@^dv;3}#4 zmWX5m(v<1))YaWxE&HQ1aqh$`Pg1$3r&itNngdemHu9+KE*bIRmMH}AG?nS6Wv7307`~v>I|6Ddb(XEZPU7^5hAkA=mn%>I z{=HOqasyF%sg!BDa}u8qAREyWjfT$c$}lFfv-_EJ<0CNiz$K4kA~NN17#>b8W4Fm2 zmA8e+Iz4|ge@gA*yMHF}x$TLvy+Yz~n-Y1vxZv#hZC3wrl&^jSI3Qrfn@b0lq&(~W zrEgJlCz~5(UZ+~YMm)MI#p8AD6 z6Th;61tuu`3&yR_0S#$bOv|tUwc^;4(Q8`BJ%z;U#7Gc9r456|JSz8X10yN*q7=g( zet7GCh^dUger2Z1ZQpSD>~m_Xs~TvaM8CG4Pzs_cu$Q8|*eio{^LG+V+%~1(Z#Zw0 z70Mk~D^`j*iWB_2SlNnu|BE2iYr~BdcTnT0V7*&sVd40*0K3B|<&Rje=bc#qoc{4c zJ^HB*9|UzWnLl~ut{@^*Q!GjDR-M&+d2Xoq12?raBxE^m=8OF3M-J)uxsg=`>guGK zZkZ!xs=30v#Zu~D^eKREDF-=!5y0Rk1@c-4E$PSRhTZw|^PCMcAm6@>1u zd6oV;*)wjvw@-m9nwsZqu{HQlQyq3d#kXy9-W@3$1`ghCj@JR3#hI+V@wKrgV`CMa z6vKT!a&rV6?rZ_4n{)X*uih?B%|= zYnWt@45k}^c^R@?sV_NGk1>CEkuSmGe8TYbRB~ps{HVFCpIPhlCqzY=3uf3ltE{ZU zvW#N51Nd;V*4OXt$ZUTQAh%gOLxftA^WcBss$m6TqZ38!Jv z9^QBEgRnv8;m~jo?6VS2n_hV5D%0&ewnoEH+d_o6p_<`Ba_^>ODejv#lnt87ZQhaT zgruK81?VLt(6YAa_J0^Q!;`4yX`U4;bWSm~=%V!*w&XWrfJE;t@>>NJ+ug zccfJ;RmYYsR_xnL(d#lSpB+L-Vax9SJhqCU@-Au@Onqv(4^$t0q^(60Uh!o`{^jxq z0jkt$1y&NwhRDgAAMq_oWgbCb3E6F19F`892@?TVY+kd(L5tQx-$nb{l$$)*1uZ5X z=FEfh0Lp#InhA?WcfzHBG?r6&5%&51W^RMlkMfFIL&4B!kuYLe^?yD8_>GWI$ZtsV#DPSNT-Ttbvfo zUnS(RwW)b{I0{>6Y{F5FpFe9qIrQuVQIqubeS~8q6`beiQptagTHt`s9EHZjKlFzU zGYAQt4#0>!_e8mOAG(&TtrrIIV!_@eVbPp4Zh#{fDv(OoAr{(-&z}v+6Xq{az^L=Q zOz0!>K1KxhRrGYz$%-CI!-HevhY*Oy+{zT2w-GO)E6XM{!WebR4HsdKlU4`M(8=rF z3Z+`8&EeuiXLgu{O?KL>V(Fmbi%mc++zhMRIC$@y>u=omiTlP8%Awu$VvY2L>jo}z zY6M8tyQYUm{my6_MFR3X&mg-7;k8 zM~cK0mI$F&U`4coH*Dxr!t-r%0>noCZI9Eze6$?*E$Z$p7K1#p^lCvd3qV!&xEo_jH2 zYGT{r0RuOWe1IJlEL6?qmQTCa+ojIp)z@c>;sL^8;R@pMSYl)zM6ow~UkPz*(Y1Ku zQa-azR!MHwNqfwz#avp;B4^ApDPX`N(}efd|B(6bbDaZ$9dvU2Jl)dsnA3Y~G8CC9ai zvp2rNY-x#!-0vc>&l#~V?5T9aeG^ktRo5bA%yK+cbo^tsWXk>HeI%67Ua#JF1nhs3 zp`keXmYw-tQamo7uLoj{6a1iqpHPd_+6P0NPoof^`#M@?tb+MtsLCT?Eamb3a^uXa zI1!WN=59DiXIesU&m)9kJZ=3{0$HB?P9D(O&)bn3i0SEdgi{_xo=bmTJzYX zJOz2jh&=$4U%L0b={ZRFyBq>Z6{hjH^%tXkLHFt5KQ0s(%(O(dcWV4wiCgG zk-^0N9$6ostD{|!b;H4*QEx{DDrMo8+it9w_?$?f5Hevg(C}W&F>8roi^;Q*iS)v< zV`H%zg@f9Z795eTwM$&9-(Mek zWXiRk6Q}ESOqZYWbxe?{_nmd+ukmWF<@%5tZc!naE0Ufk4UjM$3MWV90+^DM~6_g=z4M<0A4U12GMA2zm zNeJ!j&NtNu1&6hA;hPADTt-Ye7O%U~jX3Aog3;&mfB!ygxG|tYJcVBVVq$S8YTKFm zu18lvjKS@$K40b>2Le_Z4?LiCeh5c~39STk?#9zS$cccJLm+W;&;b%1ikZI+d{Gb) zmU^KrFzC~WNFBprhZ>7Nq$l6T>mjo;5oC!H?6FFQzDv&&EfN+IwB%9r2ka;k>cLp6 zv_zqN+I^yb>o4K)?AmN$p+Fl_cnQk}7rIxVgd-H=P^$b-!3YxiI|-mSoaRYq;;Xn5 zbedS5$CUKdv7(~lt=^A7OTh{PpaLzU!KDZe!px4VO4Pk^k%UBIJ<{_7OfFw^9NYwi z+(=J@NC8h3kcA#@`m8nZSI~lHw|Fj>wB9Il^Q=H4sd_xNzVKfX}yk&v1%o<|*ht2r~%dknsWB5SfP)aLi!u9v@t z4iC3szbY5;uIA&Jv}Qt^_AOSfg~FecHSCY1l&Ze+a$Rj$71uf&N zk}pQ_)UWR(-lDUfvXMk_6|!fcxvJ>lpLO| z29m^~?<8PrFC3)U&#*U<_{ zw$bY^mo!aHupGFLuWJj=G543hAi!acRmdXrqmDXj=f4x#g%YQccdcOhy=(JBV+W*T zXoA~mcg3$h_ZSC06$pMv>A~UzGc4)Bi?*z63O#TFbAS?u6gFm$QF-cAZMUhx48ap%N>{4P6c~tbZ;gtRUV3|i9tEF>yaW} z?dHj3I{L5^&4}H2w&@WZ_>F`_+=kl>IUM!V(|2v$;kT=hLX2+2j#4?zp!m&;j^`fv z<<77}Ii3BOLDOzg{Y)PCfcR5~V|kxlkCN|geqxCCsUs)-_G%%Vb0mf<0&Y|f1pyMA z1O^9y#~HZiG=s!pRO&inm1NUcE1YX{w}@y889><^>5>W$Ec}6SJ09HB)n&icWm;mv zz5@N5IfA$fh6cF}K)5+m%(=}FDH`QUyr zN7ZQDx^^#)Mbb4dg+k$tV`lw!ZmUAlWcjis0SKn8RiloYR@(oVRHc_qm$vOtHLwy% zMV|>Z7Xr2+{fj?t>-wFQnP9ZpI*}-`iDvr;698TjQL*R&vX}nV5IuN9(1!Uqlpwfy z$obsNA2@KJwE8u_oooB}y+x51N9eZ`@ zqodOVl%1>DLUltZSPAY@0cvz%l*3Rg^!tw=s=V{=ZR(>R{ldZ7x!l9;ZTJc%EC}Tq z5*aG>LdMH5MIi9lEdrArK~}T^BG~{$wk4BtG#+*Eu_^WB6FWcs{`ddp(|6u+WAz6= zcp{6<`Bs2>4WRZ4aXiy=sa$aWVcdATe@(YDJUn4{ccxBWb@kv|@FlV&4v}%p^~gvo zDel8cT&KMdu0(DKh<+EIM*Bod2S z`Fyc@^5n=f5B&W%KJ^Q~@R7&xm9Ro@Z{PgEgU1%|<+B3+G!wK^{A_k=czA5=ndc6SfA+KA-lPiSgtDtyBYYh$Zc^~JyQogD;K ztQR4_{KfY<niDVvNAb2R@%AqD8VhK z)9Gp^lOc$PuGuPAq;=wYUJ*cp?HVgJpxV8?Duh#&oL9qdee3lAF&v$km=5pQah!Qv z#Bttb$T~si;xn%Gje~vl&c604J}8AZ$IF#NhmKW7N9E{f6+qSiqydrPQa~DuG-0rv zS9QEuDVI`M(>6on%|gk5M&Lr*x33R(clU)73CF=-Q{eZM@wiJiltf-UOLc4cYCVUs zcY1oNwr}5v0ZYR6_ICV9%=tP#9%b?glo?h{XuxX@rHz&HW0d+z$Qx|i02&PKfdOTY z$j1@=6)}M(4MRG{g8(p2kCTNRI6Y|BXJ%$3ZSuX)&;>&jE#k%WigQ%RE9rvmGj7r* zZUD3ZF8&z0e6UYwuplzDsK!49f{#I3Q!a*Ux*$-&cyn1W%{U$DSF8&ti0`LI%r%LI;5`aRVml&X#BR7#fpaaiLMpt3mLfEGE8GNO?_JQ1&1ot>Pxngr;tD z+T^deu$59?$%|-~CzuY#DPwb*dCkC_Z<;(-v}>i5SHlG@CD&5QnGe~o`vLM}x zi=U5zUa5<_5HkL&1@M&uHq)$ literal 0 HcmV?d00001 From f2a42bd7351583b9fd45b79055eb775afa126239 Mon Sep 17 00:00:00 2001 From: Todd J Treangen Date: Tue, 10 Feb 2015 18:32:58 -0500 Subject: [PATCH 2/3] Update quickstart.rst --- docs/content/harvest/quickstart.rst | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/docs/content/harvest/quickstart.rst b/docs/content/harvest/quickstart.rst index b15fb1a..2d69126 100644 --- a/docs/content/harvest/quickstart.rst +++ b/docs/content/harvest/quickstart.rst @@ -81,7 +81,28 @@ Primary output files #. Compressed binary archive (GGR) +Additional output files +------------- - +1. Variant Call Format (.vcf)) + + Example VCF output file: :: + + ##FILTER= + ##FILTER= + ##FILTER= + ##FILTER= + ##FILTER= 20 indels"> + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT England1.fna.ref Al-Hasa_18_2013.fna Al-Hasa_1_2013.fna England-Qatar_2012.fna KSA-CAMEL-376.fna NC_019843.2.fna + gi|471258596|gb|KC164505.2| 1603 GTACTATGTA.CTTTGTGCCT C T 40 PASS NA GT 0 0 0 0 1 0 + gi|471258596|gb|KC164505.2| 1684 GGAACAAGGT.CACTCAAATT C T 40 PASS NA GT 0 0 0 0 1 0 + gi|471258596|gb|KC164505.2| 2502 ATATTCCCAT.CGGGAACCTA C T 40 PASS NA GT 0 0 0 0 1 0 + gi|471258596|gb|KC164505.2| 3275 TTCTCATGAG.ATTTCTGACG A G 40 PASS NA GT 0 1 1 0 1 0 + gi|471258596|gb|KC164505.2| 4396 TTCAAGCAGG.GAGTGTCGTG G T 40 PASS NA GT 0 1 1 0 0 0 + + . + . + . + From c16a340e36e5f30ae56e47369531f60970bc5537 Mon Sep 17 00:00:00 2001 From: Todd J Treangen Date: Fri, 20 Mar 2015 19:29:37 -0400 Subject: [PATCH 3/3] update to params --- docs/content/parsnp/quickstart.rst | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/content/parsnp/quickstart.rst b/docs/content/parsnp/quickstart.rst index 5b775fe..9315aba 100644 --- a/docs/content/parsnp/quickstart.rst +++ b/docs/content/parsnp/quickstart.rst @@ -97,10 +97,9 @@ LCB alignment:: -n = : alignment program (default: libMUSCLE) -u = : output unaligned regions? .unaligned (default: NO) -SNP filters:: +Recombination filtration:: - -R = : enable (R)epeat filtering? - -x = : enable recombination filtering? (default: NO) + -x = : enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO) Misc::