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Is it proper to count the Omer together with a Minyan?
It is proper to count the Sefira together with the Minyan. [Thus, one should not leave the Minyan for Maariv until after Sefira.]
If the Minyan is holding by Sefira and one has not yet begun Maariv is he to recite Sefira with the Tzibur?
If one came late to Shul and the congregation has reached Sefiras Haomer prior to him beginning Maariv, then in the event that he will not be Davening with another Minyan, some Poskim rule that he is to count Sefira together with the Minyan and Daven Maariv afterwards,. The same applies if he skipped Kerias Shema in order to begin Shemoneh Esrei together with the Minyan, that he should count Sefira together with the Minyan, prior to reciting Shema. Other Poskim however rule that one is to always precede Maariv to counting Sefira, even if it means that he will lose the opportunity to count with a Minyan. Practically, if one suspects he may forget to count Sefira after his private Davening, he is to count with the Minyan before Maariv.
 Shelah brought in Chok Yaakov 489/16 “Sefira with a Minyan”; Beir Heiytiv 489/20; Siddur Yaavetz “Sefira with Rov Am”; Minchas Yitzchak 9/56; See Piskeiy Teshuvos 489/3
 See Piskeiy Teshuvos 489/3
 Meiam Loez Vayikra p. 278; Moed Lekol Chaiy; Divrei Hageonim 39 in name of Derech Hachaim; Minchas Yitzchak 9/56; Orchos Rabbeinu 2/94 that so ruled Chazon Ish
 The reason: As it is proper to count the Omer with a Minyan [Poskim ibid] and one should not separate from the Tzibur. [ibid]
 Minchas Yitzchak 9/56; Orchos Rabbeinu 2/94 that so ruled Chazon Ish; To note however that many are accustomed never to skip the order of Maariv and so is the Chabad custom. [Kaf Hachaim 236/22; Ketzos Hashulchan 27 footnote 27]
 Teshuvos Vehanhagos 1/310; 2/248
 The reason: As Maariv is Tadir, and one may not precede a non-Tadir to a Tadir. [ibid]
 Piskeiy Teshuvos ibid footnote 16